Antonio Colaprico
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TCGAbiolinks |
| Branch: RELEASE_3_8 |
| Last Commit: c51253f |
| Last Changed Date: 2019-03-20 10:11:14 -0400 (Wed, 20 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:25:48 -0400 (Sat, 13 Apr 2019).
| Package 1546/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAbiolinks 2.10.5 Antonio Colaprico
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: TCGAbiolinks |
| Version: 2.10.5 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.10.5.tar.gz |
| StartedAt: 2019-04-13 05:52:54 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:23:47 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 1852.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAbiolinks.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.10.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.10.5'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 3.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'purrr'
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'move'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCquery_clinic: no visible binding for global variable 'portions'
TCGAanalyze_DEA: no visible binding for global variable 'barcode'
TCGAanalyze_DEA: no visible binding for global variable 'clinical'
TCGAanalyze_DEA_Affy: no visible global function definition for
'limmamakeContrasts'
TCGAanalyze_DEA_Affy: no visible global function definition for
'limmacontrasts.fit'
TCGAanalyze_analyseGRN: no visible global function definition for
'knnmi.cross'
TCGAanalyze_networkInference: no visible global function definition for
'c3net'
TCGAanalyze_networkInference: no visible global function definition for
'minet'
TCGAquery_recount2: no visible binding for global variable 'rse_gene'
TCGAtumor_purity: no visible binding for global variable 'Tumor.purity'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'dNetInduce'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'dNetPipeline'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'dCommSignif'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'visNet'
TCGAvisualize_oncoprint: no visible binding for global variable 'value'
readExonQuantification: no visible binding for global variable 'exon'
readExonQuantification: no visible binding for global variable
'coordinates'
Undefined global functions or variables:
Tumor.purity barcode c3net clinical coordinates dCommSignif
dNetInduce dNetPipeline exon knnmi.cross limmacontrasts.fit
limmamakeContrasts minet portions rse_gene value visNet
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_LevelTab 19.32 0.07 19.37
TCGAanalyze_DMR 15.06 0.17 15.24
TCGAanalyze_Filtering 13.76 0.03 13.80
TCGAanalyze_DEA 12.05 0.23 12.28
TCGAvisualize_PCA 7.74 0.02 7.79
GDCprepare_clinic 7.67 0.04 50.20
TCGAanalyze_Normalization 7.61 0.00 7.61
GDCdownload 4.69 0.33 33.41
getResults 2.92 0.00 7.88
getManifest 2.78 0.12 7.46
GDCquery 2.86 0.00 7.27
GDCprepare 2.51 0.33 6.65
matchedMetExp 2.72 0.00 7.65
getSampleFilesSummary 2.48 0.13 8.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_DMR 19.09 0.07 19.36
TCGAanalyze_LevelTab 18.28 0.05 18.36
TCGAanalyze_Filtering 14.32 0.00 14.34
TCGAanalyze_DEA 10.17 0.03 10.20
GDCprepare_clinic 9.63 0.18 51.00
TCGAvisualize_PCA 6.83 0.00 6.84
TCGAanalyze_Normalization 5.79 0.00 5.80
GDCdownload 4.14 0.19 33.39
getSampleFilesSummary 2.45 0.05 7.50
getManifest 2.06 0.02 6.78
GDCquery 1.90 0.00 15.36
getResults 1.64 0.00 6.20
matchedMetExp 1.60 0.01 6.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.
TCGAbiolinks.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/TCGAbiolinks_2.10.5.tar.gz && rm -rf TCGAbiolinks.buildbin-libdir && mkdir TCGAbiolinks.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.10.5.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TCGAbiolinks_2.10.5.zip && rm TCGAbiolinks_2.10.5.tar.gz TCGAbiolinks_2.10.5.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 9294k 100 9294k 0 0 50.8M 0 --:--:-- --:--:-- --:--:-- 51.8M
install for i386
* installing *source* package 'TCGAbiolinks' ...
** R
Warning in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, :
internal error 10 in R_compress3
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TCGAbiolinks'
finding HTML links ... done
BRCA_rnaseqv2 html
GDCdownload html
GDCprepare html
GDCprepare_clinic html
GDCquery html
GDCquery_ATAC_seq html
GDCquery_Maf html
GDCquery_clinic html
GeneSplitRegulon html
GenesCutID html
PanCancerAtlas_subtypes html
TCGAVisualize_volcano html
TCGA_MolecularSubtype html
TCGAanalyze_Clustering html
TCGAanalyze_DEA html
TCGAanalyze_DEA_Affy html
TCGAanalyze_DMR html
TCGAanalyze_EA html
TCGAanalyze_EAcomplete html
TCGAanalyze_Filtering html
TCGAanalyze_LevelTab html
TCGAanalyze_Normalization html
TCGAanalyze_Pathview html
TCGAanalyze_Preprocessing html
TCGAanalyze_SurvivalKM html
TCGAanalyze_analyseGRN html
TCGAanalyze_networkInference html
TCGAanalyze_survival html
TCGAbatch_Correction html
TCGAbiolinks html
TCGAprepare_Affy html
TCGAquery_MatchedCoupledSampleTypes html
TCGAquery_SampleTypes html
TCGAquery_recount2 html
TCGAquery_subtype html
TCGAtumor_purity html
TCGAvisualize_BarPlot html
TCGAvisualize_EAbarplot html
TCGAvisualize_Heatmap html
TCGAvisualize_PCA html
TCGAvisualize_SurvivalCoxNET html
TCGAvisualize_meanMethylation html
TCGAvisualize_oncoprint html
TCGAvisualize_starburst html
TabSubtypesCol_merged html
Tumor.purity html
UseRaw_afterFilter html
batch.info html
bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf
html
calculate.pvalues html
chol_maf html
clinBRCA html
clinical.biotab html
colDataPrepare html
dataBRCA html
dataDEGsFiltLevel html
dataREAD html
dataREAD_df html
diffmean html
gaiaCNVplot html
gbm.exp.harmonized html
gbm.exp.legacy html
geneInfo html
geneInfoHT html
get.GRCh.bioMart html
getAdjacencyBiogrid html
getDataCategorySummary html
getGDCInfo html
getGDCprojects html
getGistic html
getManifest html
getResults html
getSampleFilesSummary html
getTSS html
get_IDs html
ggbiplot html
isServeOK html
matchedMetExp html
met.gbm.27k html
msi_results html
pancan2018 html
tabSurvKMcompleteDEGs html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'TCGAbiolinks' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAbiolinks' as TCGAbiolinks_2.10.5.zip
* DONE (TCGAbiolinks)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TCGAbiolinks' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
TCGAbiolinks.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
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<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-ACC/harmonized/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/9d298cc7-71d2-43f5-835d-d7ef7a43bb11/TCGA.ACC.muse.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.DR-10.0.somatic.maf.gz', reason 'No such file or directory'>
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<simpleWarning in file.create(to[okay]): cannot create file 'maf/TCGA-ACC/harmonized/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/9d298cc7-71d2-43f5-835d-d7ef7a43bb11/TCGA.ACC.muse.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.DR-10.0.somatic.maf.gz', reason 'No such file or directory'>
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[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"
groups Mean Median Max Min
1 TP 0.3590198 0.3601768 0.4099433 0.3240056
groups Mean Median Max Min
1 TP 0.3590198 0.3601768 0.4099433 0.3240056
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 alive 0.3594683 0.3594683 0.3594683 0.3594683
2 dead 0.3589557 0.3608853 0.4099433 0.3240056
alive dead
alive NA NA
dead NA NA
== testthat results ===========================================================
OK: 69 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
166.71 3.62 463.36
|
TCGAbiolinks.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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> library(testthat)
> library(TCGAbiolinks)
>
> test_check("TCGAbiolinks")
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<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-ACC/harmonized/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/9d298cc7-71d2-43f5-835d-d7ef7a43bb11/TCGA.ACC.muse.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.DR-10.0.somatic.maf.gz', reason 'No such file or directory'>
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<simpleWarning in file.create(to[okay]): cannot create file 'maf/TCGA-ACC/harmonized/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/9d298cc7-71d2-43f5-835d-d7ef7a43bb11/TCGA.ACC.muse.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.DR-10.0.somatic.maf.gz', reason 'No such file or directory'>
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[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"
groups Mean Median Max Min
1 TP 0.3590198 0.3601768 0.4099433 0.3240056
groups Mean Median Max Min
1 TP 0.3590198 0.3601768 0.4099433 0.3240056
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 LGm1 0.3789137 0.3789137 0.3789137 0.3789137
2 LGm2 0.4099433 0.4099433 0.4099433 0.4099433
3 LGm4 0.3454189 0.3454189 0.3668322 0.3240056
4 LGm5 0.3481159 0.3524203 0.3608853 0.3267376
LGm1 LGm2 LGm4 LGm5
LGm1 NA NA NA NA
LGm2 NA NA NA NA
LGm4 NA NA NA 0.9217168
LGm5 NA NA 0.9217168 NA
groups Mean Median Max Min
1 alive 0.3594683 0.3594683 0.3594683 0.3594683
2 dead 0.3589557 0.3608853 0.4099433 0.3240056
alive dead
alive NA NA
dead NA NA
== testthat results ===========================================================
OK: 69 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
147.64 1.65 461.00
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