| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q R S [T] U V W X Y Z |
This page was generated on 2017-08-16 13:24:51 -0400 (Wed, 16 Aug 2017).
| Package 1308/1382 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| TCGAbiolinks 2.5.7 Antonio Colaprico
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK |  | |||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TCGAbiolinks |
| Version: 2.5.7 |
| Command: rm -rf TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && mkdir TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.5.7.tar.gz >TCGAbiolinks.Rcheck\00install.out 2>&1 && cp TCGAbiolinks.Rcheck\00install.out TCGAbiolinks-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TCGAbiolinks.buildbin-libdir --install="check:TCGAbiolinks-install.out" --force-multiarch --no-vignettes --timings TCGAbiolinks_2.5.7.tar.gz |
| StartedAt: 2017-08-16 03:16:22 -0400 (Wed, 16 Aug 2017) |
| EndedAt: 2017-08-16 03:39:12 -0400 (Wed, 16 Aug 2017) |
| EllapsedTime: 1370.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TCGAbiolinks.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && mkdir TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.5.7.tar.gz >TCGAbiolinks.Rcheck\00install.out 2>&1 && cp TCGAbiolinks.Rcheck\00install.out TCGAbiolinks-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TCGAbiolinks.buildbin-libdir --install="check:TCGAbiolinks-install.out" --force-multiarch --no-vignettes --timings TCGAbiolinks_2.5.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.5.7'
* 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 whether package 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
installed size is 65.7Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 6.4Mb
doc 58.0Mb
* 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 ... OK
* 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_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'
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'
Undefined global functions or variables:
c3net dCommSignif dNetInduce dNetPipeline knnmi.cross
limmacontrasts.fit limmamakeContrasts minet portions 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'TCGAbiolinks-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GDCquery_Maf
> ### Title: Retrieve open access maf files from GDC server
> ### Aliases: GDCquery_Maf
>
> ### ** Examples
>
> acc.muse.maf <- GDCquery_Maf("ACC", pipelines = "muse")
============================================================================
For more information about MAF data please read the following GDC manual and web pages:
GDC manual: https://gdc-docs.nci.nih.gov/Data/PDF/Data_UG.pdf
https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
https://gdc.cancer.gov/about-gdc/variant-calling-gdc
============================================================================
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-ACC
--------------------
oo Filtering results
--------------------
ooo By access
ooo By data.type
ooo By workflow.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
Downloading data for project TCGA-ACC
GDCdownload will download: 2.041717 MB
Downloading as: TCGA.ACC.muse.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.DR-7.0.somatic.maf.gz
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|======================================================================| 100%<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-ACC/harmonized/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/c9d7ed14-11a0-49b3-a17f-e843c2a5cd88/TCGA.ACC.muse.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.DR-7.0.somatic.maf.gz', reason 'No such file or directory'>
Error in GDCprepare(query, directory = directory) :
I couldn't find all the files from the query. Please check if the directory parameter right or GDCdownload downloaded the samples.
Calls: GDCquery_Maf -> GDCprepare
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'TCGAbiolinks-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TCGAvisualize_oncoprint
> ### Title: Creating a oncoprint
> ### Aliases: TCGAvisualize_oncoprint
>
> ### ** Examples
>
> mut <- GDCquery_Maf(tumor = "ACC", pipelines = "mutect")
============================================================================
For more information about MAF data please read the following GDC manual and web pages:
GDC manual: https://gdc-docs.nci.nih.gov/Data/PDF/Data_UG.pdf
https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
https://gdc.cancer.gov/about-gdc/variant-calling-gdc
============================================================================
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-ACC
--------------------
oo Filtering results
--------------------
ooo By access
ooo By data.type
ooo By workflow.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
Downloading data for project TCGA-ACC
GDCdownload will download: 2.327242 MB
Downloading as: TCGA.ACC.mutect.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.DR-7.0.somatic.maf.gz
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|======================================================================| 100%<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-ACC/harmonized/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/ac3a9f5a-d78e-4b13-acb8-1001b215ffb6/TCGA.ACC.mutect.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.DR-7.0.somatic.maf.gz', reason 'No such file or directory'>
Error in GDCprepare(query, directory = directory) :
I couldn't find all the files from the query. Please check if the directory parameter right or GDCdownload downloaded the samples.
Calls: GDCquery_Maf -> GDCprepare
Execution halted
* 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 ... NOTE
'library' or 'require' call not declared from: 'DT'
* 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: 2 ERRORs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.
TCGAbiolinks.Rcheck/00install.out:
install for i386 * installing *source* package 'TCGAbiolinks' ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'TCGAbiolinks' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'TCGAbiolinks' as TCGAbiolinks_2.5.7.zip * DONE (TCGAbiolinks)
TCGAbiolinks.Rcheck/examples_i386/TCGAbiolinks-Ex.timings:
| name | user | system | elapsed | |
| GDCdownload | 7.88 | 1.05 | 52.99 | |
| GDCprepare | 6.75 | 0.28 | 10.75 | |
| GDCprepare_clinic | 5.06 | 0.04 | 8.60 | |
| GDCquery | 19.28 | 0.07 | 26.08 | |
TCGAbiolinks.Rcheck/examples_x64/TCGAbiolinks-Ex.timings:
| name | user | system | elapsed | |
| GDCdownload | 9.09 | 1.34 | 59.39 | |
| GDCprepare | 11.38 | 0.19 | 15.40 | |
| GDCprepare_clinic | 5.97 | 0.05 | 8.83 | |
| GDCquery | 21.61 | 0.03 | 28.78 | |
| GDCquery_Maf | 1.41 | 0.01 | 3.48 | |
| GDCquery_clinic | 1.19 | 0.03 | 3.18 | |
| TCGAVisualize_volcano | 9.12 | 0.02 | 9.17 | |
| TCGAanalyze_DEA | 13.94 | 0.08 | 14.01 | |
| TCGAanalyze_DEA_Affy | 0 | 0 | 0 | |
| TCGAanalyze_DMR | 21.05 | 0.19 | 21.30 | |
| TCGAanalyze_EA | 0 | 0 | 0 | |
| TCGAanalyze_EAcomplete | 4 | 0 | 4 | |
| TCGAanalyze_Filtering | 13.05 | 0.01 | 13.06 | |
| TCGAanalyze_LevelTab | 20.59 | 0.03 | 20.62 | |
| TCGAanalyze_Normalization | 5.89 | 0.00 | 5.89 | |
| TCGAanalyze_Pathview | 0 | 0 | 0 | |
| TCGAanalyze_SurvivalKM | 2.84 | 0.03 | 11.52 | |
| TCGAanalyze_survival | 6.92 | 0.08 | 9.81 | |
| TCGAprepare_Affy | 0 | 0 | 0 | |
| TCGAprepare_elmer | 0.02 | 0.00 | 0.01 | |
| TCGAquery_MatchedCoupledSampleTypes | 0.03 | 0.00 | 0.03 | |
| TCGAquery_SampleTypes | 0 | 0 | 0 | |
| TCGAquery_subtype | 0.02 | 0.00 | 0.02 | |
| TCGAvisualize_EAbarplot | 3.26 | 0.00 | 3.27 | |
| TCGAvisualize_Heatmap | 3.61 | 0.00 | 3.61 | |
| TCGAvisualize_PCA | 5.75 | 0.00 | 5.75 | |
| TCGAvisualize_meanMethylation | 4.15 | 0.00 | 4.16 | |