| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2076/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.28.4 (landing page) Tiago Chedraoui Silva
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the TCGAbiolinks package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: TCGAbiolinks |
| Version: 2.28.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.28.4.tar.gz |
| StartedAt: 2023-10-19 06:14:39 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 06:29:08 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 868.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.28.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TCGAbiolinks.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.28.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TCGAbiolinks’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 4.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCprepare_clinic: no visible binding for global variable
‘bcr_patient_barcode’
GDCprepare_clinic: no visible binding for global variable
‘days_to_last_followup’
GDCprepare_clinic: no visible binding for global variable
‘vital_status’
GDCquery : <anonymous>: no visible binding for global variable
‘submitter_id’
GDCquery : <anonymous>: no visible binding for global variable
‘is_ffpe’
GDCquery_clinic : <anonymous>: no visible binding for global variable
‘submitter_id’
GDCquery_clinic : <anonymous>: no visible global function definition
for ‘across’
GDCquery_clinic : <anonymous>: no visible global function definition
for ‘everything’
TCGAanalyze_DEA: no visible binding for global variable ‘barcode’
TCGAanalyze_DEA: no visible binding for global variable ‘clinical’
TCGAquery_recount2: no visible binding for global variable ‘rse_gene’
TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
TCGAvisualize_starburst: no visible binding for global variable
‘gene_name’
TCGAvisualize_starburst: no visible binding for global variable
‘geFDR2’
TCGAvisualize_starburst: no visible binding for global variable ‘logFC’
TCGAvisualize_starburst: no visible binding for global variable
‘meFDR2’
TCGAvisualize_starburst: no visible binding for global variable
‘threshold.starburst’
TCGAvisualize_starburst: no visible binding for global variable
‘starburst.status’
colDataPrepare: no visible binding for global variable
‘sample_submitter_id’
colDataPrepare: no visible binding for global variable ‘submitter_id’
readExonQuantification: no visible binding for global variable ‘exon’
readExonQuantification: no visible binding for global variable
‘coordinates’
readSingleCellAnalysis : <anonymous>: no visible global function
definition for ‘Read10X’
read_gene_expression_quantification : <anonymous>: no visible binding
for '<<-' assignment to ‘assay.list’
read_gene_expression_quantification: no visible binding for global
variable ‘assay.list’
Undefined global functions or variables:
Read10X Tumor.purity across assay.list barcode bcr_patient_barcode
clinical coordinates days_to_last_followup everything exon geFDR2
gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id
starburst.status submitter_id threshold.starburst value vital_status
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getManifest 11.687 0.582 103.901
TCGAanalyze_DEA 11.285 0.337 20.572
TCGAanalyze_LevelTab 6.070 0.085 10.980
TCGAanalyze_Filtering 4.770 0.060 8.578
TCGAvisualize_meanMethylation 3.389 0.060 6.035
TCGAanalyze_survival 3.124 0.108 5.799
TCGAanalyze_EAcomplete 2.754 0.078 5.005
GDCprepare_clinic 1.194 0.147 41.165
matchedMetExp 1.108 0.062 14.578
getDataCategorySummary 1.061 0.018 8.556
GDCquery_clinic 0.910 0.042 8.497
GDCquery 0.752 0.036 9.690
getResults 0.751 0.026 8.354
getSampleFilesSummary 0.501 0.032 5.612
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Failure ('test-analyse.R:153:9'): Results of TCGAanalyze_DEA inverting groups changes signal and order of the signals are right ──
dataDEGs$logFC not equal to -1 * dataDEGs.inv$logFC.
8/15396 mismatches (average diff: 0.852)
[7378] 0.638 - -0.634 == 1.272
[7379] -0.634 - 0.638 == -1.272
[9519] -0.429 - 0.429 == -0.858
[9520] 0.429 - -0.429 == 0.858
[10555] 0.365 - -0.355 == 0.720
[10556] -0.355 - 0.365 == -0.720
[11525] 0.279 - -0.279 == 0.558
[11526] -0.279 - 0.279 == -0.558
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 31 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
TCGAbiolinks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TCGAbiolinks ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘TCGAbiolinks’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TCGAbiolinks)
TCGAbiolinks.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(TCGAbiolinks)
>
> test_check("TCGAbiolinks")
| | 0%
|========================== | 50% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
| | 0%
|========================== | 50% ~0 s remaining
|====================================================|100% ~0 s remaining
|====================================================|100% Completed after 0 s
[1] "I need about 1 minute to finish complete Enrichment analysis GO[BP,MF,CC] and Pathways... "
[1] "GO Enrichment Analysis BP completed....done"
[1] "GO Enrichment Analysis MF completed....done"
[1] "GO Enrichment Analysis CC completed....done"
[1] "Pathway Enrichment Analysis completed....done"
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 31 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On Bioconductor (24): 'test-prepare-download.R:4:5',
'test-prepare-download.R:49:5', 'test-prepare-download.R:92:5',
'test-prepare-download.R:102:5', 'test-prepare-download.R:124:5',
'test-prepare-download.R:145:5', 'test-prepare-download.R:164:5',
'test-prepare-download.R:183:5', 'test-prepare-download.R:199:5',
'test-prepare-download.R:209:5', 'test-prepare-download.R:221:5',
'test-prepare-download.R:246:5', 'test-prepare-download.R:286:5',
'test-prepare-download.R:316:5', 'test-prepare-download.R:347:5',
'test-prepare-download.R:381:5', 'test-query-clinical.R:13:5',
'test-query-clinical.R:69:5', 'test-query.R:5:5', 'test-query.R:15:5',
'test-query.R:44:5', 'test-query.R:86:5', 'test-query.R:127:5',
'test-query.R:147:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-analyse.R:153:9'): Results of TCGAanalyze_DEA inverting groups changes signal and order of the signals are right ──
dataDEGs$logFC not equal to -1 * dataDEGs.inv$logFC.
8/15396 mismatches (average diff: 0.852)
[7378] 0.638 - -0.634 == 1.272
[7379] -0.634 - 0.638 == -1.272
[9519] -0.429 - 0.429 == -0.858
[9520] 0.429 - -0.429 == 0.858
[10555] 0.365 - -0.355 == 0.720
[10556] -0.355 - 0.365 == -0.720
[11525] 0.279 - -0.279 == 0.558
[11526] -0.279 - 0.279 == -0.558
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 31 ]
Error: Test failures
Execution halted
TCGAbiolinks.Rcheck/TCGAbiolinks-Ex.timings
| name | user | system | elapsed | |
| GDCdownload | 0.000 | 0.000 | 0.001 | |
| GDCprepare | 0.000 | 0.000 | 0.004 | |
| GDCprepare_clinic | 1.194 | 0.147 | 41.165 | |
| GDCquery | 0.752 | 0.036 | 9.690 | |
| GDCquery_ATAC_seq | 0.368 | 0.038 | 2.060 | |
| GDCquery_clinic | 0.910 | 0.042 | 8.497 | |
| PanCancerAtlas_subtypes | 0.016 | 0.002 | 0.031 | |
| TCGAVisualize_volcano | 0.962 | 0.035 | 1.979 | |
| TCGA_MolecularSubtype | 0.357 | 0.004 | 0.642 | |
| TCGAanalyze_DEA | 11.285 | 0.337 | 20.572 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMC | 1.137 | 0.080 | 2.174 | |
| TCGAanalyze_EA | 0.000 | 0.000 | 0.001 | |
| TCGAanalyze_EAcomplete | 2.754 | 0.078 | 5.005 | |
| TCGAanalyze_Filtering | 4.770 | 0.060 | 8.578 | |
| TCGAanalyze_LevelTab | 6.070 | 0.085 | 10.980 | |
| TCGAanalyze_Normalization | 1.643 | 0.022 | 2.962 | |
| TCGAanalyze_Pathview | 0 | 0 | 0 | |
| TCGAanalyze_Stemness | 1.955 | 0.032 | 3.518 | |
| TCGAanalyze_SurvivalKM | 0.179 | 0.009 | 0.339 | |
| TCGAanalyze_survival | 3.124 | 0.108 | 5.799 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.003 | 0.000 | 0.006 | |
| TCGAquery_SampleTypes | 0.001 | 0.001 | 0.001 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.008 | 0.000 | 0.014 | |
| TCGAtumor_purity | 0.064 | 0.001 | 0.118 | |
| TCGAvisualize_EAbarplot | 2.676 | 0.053 | 4.848 | |
| TCGAvisualize_Heatmap | 2.300 | 0.123 | 4.599 | |
| TCGAvisualize_PCA | 2.235 | 0.028 | 3.999 | |
| TCGAvisualize_meanMethylation | 3.389 | 0.060 | 6.035 | |
| TCGAvisualize_oncoprint | 0.000 | 0.000 | 0.001 | |
| TCGAvisualize_starburst | 0.000 | 0.001 | 0.003 | |
| UseRaw_afterFilter | 0 | 0 | 0 | |
| colDataPrepare | 0.148 | 0.006 | 1.521 | |
| dmc.non.parametric | 0.125 | 0.033 | 0.283 | |
| dmc.non.parametric.se | 0.249 | 0.022 | 0.495 | |
| gaiaCNVplot | 0.033 | 0.003 | 0.064 | |
| getAdjacencyBiogrid | 0.002 | 0.000 | 0.001 | |
| getDataCategorySummary | 1.061 | 0.018 | 8.556 | |
| getGDCInfo | 0.027 | 0.003 | 0.609 | |
| getGDCprojects | 0.023 | 0.012 | 0.184 | |
| getLinkedOmicsData | 0.000 | 0.001 | 0.005 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 11.687 | 0.582 | 103.901 | |
| getNbCases | 0.000 | 0.000 | 0.001 | |
| getNbFiles | 0.000 | 0.001 | 0.000 | |
| getProjectSummary | 0.050 | 0.015 | 0.586 | |
| getResults | 0.751 | 0.026 | 8.354 | |
| getSampleFilesSummary | 0.501 | 0.032 | 5.612 | |
| getTSS | 0.000 | 0.000 | 0.003 | |
| gliomaClassifier | 0 | 0 | 0 | |
| isServeOK | 0.025 | 0.002 | 0.602 | |
| matchedMetExp | 1.108 | 0.062 | 14.578 | |