CRAN Package Check Results for Package ggpicrust2

Last updated on 2026-02-13 07:50:57 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.5.2				OK
r-devel-linux-x86_64-debian-gcc	2.5.2	8.39	72.65	81.04	OK
r-devel-linux-x86_64-fedora-clang	2.5.10	25.00	219.09	244.09	OK
r-devel-linux-x86_64-fedora-gcc	2.5.10	22.00	287.81	309.81	OK
r-devel-macos-arm64	2.5.10	3.00	50.00	53.00	OK
r-devel-windows-x86_64	2.5.2	14.00	117.00	131.00	OK
r-patched-linux-x86_64	2.5.2	11.89	95.34	107.23	OK
r-release-linux-x86_64	2.5.2	11.10	96.02	107.12	OK
r-release-macos-arm64	2.5.10	3.00	49.00	52.00	ERROR
r-release-macos-x86_64	2.5.10	11.00	283.00	294.00	OK
r-release-windows-x86_64	2.5.10	16.00	174.00	190.00	OK
r-oldrel-macos-arm64	2.5.10	3.00	60.00	63.00	NOTE
r-oldrel-macos-x86_64	2.5.10	12.00	324.00	336.00	NOTE
r-oldrel-windows-x86_64	2.5.10	16.00	221.00	237.00	OK

Check Details

Version: 2.5.10
Check: tests
Result: ERROR Running ‘testthat.R’ [8s/8s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ggpicrust2) Loading required package: ggpicrust2 To cite ggpicrust2 in publications use: Chen Yang, Jiahao Mai, Xuan Cao, Aaron Burberry, Fabio Cominelli, Liangliang Zhang, ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization, Bioinformatics, Volume 39, Issue 8, August 2023, btad470, https://doi.org/10.1093/bioinformatics/btad470 > > test_check("ggpicrust2") Reading input data... Performing pathway differential abundance analysis... Annotating pathways... Creating pathway error bar plots... Plot 1 skipped (no data for method: mock_method) ggpicrust2 analysis completed. Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference. Using column 'sample_name' as sample identifier | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% Saving _problems/test-pathway_daa-32.R Saving _problems/test-pathway_daa-52.R Saving _problems/test-pathway_daa-86.R Saving _problems/test-pathway_daa-150.R Saving _problems/test-pathway_daa-181.R Saving _problems/test-pathway_daa-221.R Saving _problems/test-pathway_daa-233.R Excluded 1 pathways with missing annotations. Use 'pathway_annotation' to add them. Excluded 1 rows with missing 'pathway_name' annotations. Saving _problems/test-pathway_errorbar-232.R Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference. Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Testing 2 gene sets (filtered from 2 by size constraints) Using column 'sample' as sample identifier The Sample Names in order from left to right are: S1, S2, S3, S4 The Group Levels in order from left to right are: A, A, B, B Using column 'sample' as sample identifier The Sample Names in order from left to right are: S1, S2, S3, S4 The Group Levels in order from left to right are: A, A, B, B Using column 'sample' as sample identifier The Sample Names in order from left to right are: S1, S2, S3, S4 The Group Levels in order from left to right are: A, A, B, B Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Too few points to calculate an ellipse Too few points to calculate an ellipse Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |=============== | 22% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | |========================= | 35% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 38% | |=========================== | 39% | |============================ | 39% | |============================ | 40% | |============================ | 41% | |============================= | 41% | |============================= | 42% | |============================== | 42% | |============================== | 43% | |============================== | 44% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 48% | |================================== | 49% | |=================================== | 49% | |=================================== | 50% | |=================================== | 51% | |==================================== | 51% | |==================================== | 52% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 58% | |========================================= | 59% | |========================================== | 59% | |========================================== | 60% | |========================================== | 61% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================= | 65% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================= | 71% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |======================================================== | 81% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 89% | |=============================================================== | 90% | |=============================================================== | 91% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% [ FAIL 8 | WARN 2 | SKIP 9 | PASS 151 ] ══ Skipped tests (9) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test-pathway_ridgeplot.R:25:3', 'test-pathway_ridgeplot.R:42:3', 'test-pathway_ridgeplot.R:65:3', 'test-pathway_volcano.R:82:3' • Set GGPICRUST2_RUN_E2E_TESTS=true to run full ggpicrust2 end-to-end tests. (1): 'test-ggpicrust2-return-structure.R:4:3' • Set GGPICRUST2_RUN_EXTENDED_DAA_TESTS=true to run extended DAA method tests. (1): 'test-pathway_daa.R:102:3' • Set GGPICRUST2_RUN_NETWORK_TESTS=true to run network-dependent KEGG tests. (2): 'test-pathway_annotation.R:36:3', 'test-pathway_annotation.R:55:3' • {lefser} is not installed (1): 'test-pathway_daa.R:293:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pathway_daa.R:32:3'): pathway_daa works with basic inputs ────── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(td$abundance, td$metadata, "group", daa_method = "ALDEx2") at test-pathway_daa.R:32:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:49:3'): pathway_daa validates inputs correctly ─── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-pathway_daa.R:49:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ggpicrust2::pathway_daa(...) 8. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:86:5'): pathway_daa core methods produce expected results ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-pathway_daa.R:86:5 2. │ └─base::withCallingHandlers(...) 3. └─ggpicrust2::pathway_daa(abundance, metadata, "group", daa_method = method) 4. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:149:3'): pathway_daa handles sample selection correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:149:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:180:3'): pathway_daa handles factor levels correctly with subset ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:180:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:220:3'): pathway_daa handles p-value adjustment correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:220:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:232:3'): pathway_daa include_abundance_stats parameter works correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:232:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_errorbar.R:227:3'): pathway_errorbar_table function works correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_errorbar.R:227:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) [ FAIL 8 | WARN 2 | SKIP 9 | PASS 151 ] Error: ! Test failures. Execution halted Flavor: r-release-macos-arm64

Version: 2.5.10
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘lefser’ Flavor: r-oldrel-macos-arm64

Version: 2.5.10
Check: installed package size
Result: NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 3.6Mb extdata 1.0Mb Flavor: r-oldrel-macos-x86_64