| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:47 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 2138/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TCGAbiolinks 2.32.0 (landing page) Tiago Chedraoui Silva
| kjohnson3 | macOS 13.6.5 Ventura / 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: 2.32.0 |
| 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_2.32.0.tar.gz |
| StartedAt: 2024-05-07 01:24:56 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 01:29:40 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 284.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_2.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/TCGAbiolinks.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.32.0’
* 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:
data 4.5Mb
R 1.7Mb
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘dnet’
* checking S3 generic/method consistency ... WARNING
print:
function(x, ...)
print.header:
function(text, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colDataPrepare: no visible binding for global variable
‘sample_submitter_id’
colDataPrepare: no visible binding for global variable ‘submitter_id’
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’
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’
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’
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’
Undefined global functions or variables:
across assay.list barcode bcr_patient_barcode clinical coordinates
days_to_last_followup everything exon geFDR2 gene_name is_ffpe logFC
meFDR2 Read10X rse_gene sample_submitter_id starburst.status
submitter_id threshold.starburst Tumor.purity 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 2.818 0.099 94.675
GDCprepare_clinic 0.691 0.047 30.262
matchedMetExp 0.317 0.016 8.987
GDCquery 0.291 0.025 8.332
getResults 0.233 0.015 6.663
* 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:
10/15396 mismatches (average diff: 0.792)
[7378] -0.634 - 0.638 == -1.272
[7379] 0.638 - -0.634 == 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
[11506] -0.274 - 0.276 == -0.550
[11507] 0.276 - -0.274 == 0.550
[11525] 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 ... 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 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-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/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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.
10/15396 mismatches (average diff: 0.792)
[7378] -0.634 - 0.638 == -1.272
[7379] 0.638 - -0.634 == 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
[11506] -0.274 - 0.276 == -0.550
[11507] 0.276 - -0.274 == 0.550
[11525] 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 | 0 | 0 | |
| GDCprepare_clinic | 0.691 | 0.047 | 30.262 | |
| GDCquery | 0.291 | 0.025 | 8.332 | |
| GDCquery_ATAC_seq | 0.111 | 0.013 | 1.228 | |
| GDCquery_clinic | 0.271 | 0.014 | 2.928 | |
| PanCancerAtlas_subtypes | 0.006 | 0.000 | 0.006 | |
| TCGAVisualize_volcano | 0.096 | 0.005 | 0.101 | |
| TCGA_MolecularSubtype | 0.093 | 0.002 | 0.095 | |
| TCGAanalyze_DEA | 4.350 | 0.150 | 4.516 | |
| TCGAanalyze_DEA_Affy | 0.001 | 0.000 | 0.000 | |
| TCGAanalyze_DMC | 0.285 | 0.023 | 0.309 | |
| TCGAanalyze_EA | 0 | 0 | 0 | |
| TCGAanalyze_EAcomplete | 0.691 | 0.013 | 0.704 | |
| TCGAanalyze_Filtering | 1.448 | 0.036 | 1.485 | |
| TCGAanalyze_LevelTab | 1.714 | 0.038 | 1.752 | |
| TCGAanalyze_Normalization | 0.428 | 0.016 | 0.444 | |
| TCGAanalyze_Pathview | 0 | 0 | 0 | |
| TCGAanalyze_Stemness | 0.888 | 0.017 | 0.905 | |
| TCGAanalyze_SurvivalKM | 0.037 | 0.002 | 0.040 | |
| TCGAanalyze_survival | 0.742 | 0.020 | 0.762 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAquery_MatchedCoupledSampleTypes | 0 | 0 | 0 | |
| TCGAquery_SampleTypes | 0 | 0 | 0 | |
| TCGAquery_recount2 | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.003 | 0.000 | 0.003 | |
| TCGAtumor_purity | 0.02 | 0.00 | 0.02 | |
| TCGAvisualize_EAbarplot | 0.604 | 0.039 | 0.643 | |
| TCGAvisualize_Heatmap | 0.566 | 0.021 | 0.587 | |
| TCGAvisualize_PCA | 0.458 | 0.016 | 0.474 | |
| TCGAvisualize_meanMethylation | 0.755 | 0.010 | 0.765 | |
| TCGAvisualize_oncoprint | 0 | 0 | 0 | |
| TCGAvisualize_starburst | 0 | 0 | 0 | |
| UseRaw_afterFilter | 0 | 0 | 0 | |
| colDataPrepare | 0.040 | 0.003 | 0.534 | |
| dmc.non.parametric | 0.024 | 0.004 | 0.029 | |
| dmc.non.parametric.se | 0.040 | 0.003 | 0.043 | |
| gaiaCNVplot | 0.01 | 0.00 | 0.01 | |
| geneInfoHT | 0 | 0 | 0 | |
| getAdjacencyBiogrid | 0 | 0 | 0 | |
| getDataCategorySummary | 0.349 | 0.011 | 1.979 | |
| getGDCInfo | 0.008 | 0.001 | 0.155 | |
| getGDCprojects | 0.006 | 0.001 | 0.117 | |
| getLinkedOmicsData | 0 | 0 | 0 | |
| getMC3MAF | 0 | 0 | 0 | |
| getManifest | 2.818 | 0.099 | 94.675 | |
| getNbCases | 0 | 0 | 0 | |
| getNbFiles | 0 | 0 | 0 | |
| getProjectSummary | 0.014 | 0.002 | 0.355 | |
| getResults | 0.233 | 0.015 | 6.663 | |
| getSampleFilesSummary | 0.161 | 0.013 | 1.733 | |
| getTSS | 0 | 0 | 0 | |
| gliomaClassifier | 0.000 | 0.000 | 0.001 | |
| isServeOK | 0.007 | 0.001 | 0.129 | |
| matchedMetExp | 0.317 | 0.016 | 8.987 | |