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BioC 3.5: CHECK report for BatchQC on tokay2

This page was generated on 2017-08-16 13:25:41 -0400 (Wed, 16 Aug 2017).

Package 90/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 1.4.0
Solaiappan Manimaran
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/BatchQC
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BatchQC
Version: 1.4.0
Command: rm -rf BatchQC.buildbin-libdir BatchQC.Rcheck && mkdir BatchQC.buildbin-libdir BatchQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BatchQC.buildbin-libdir BatchQC_1.4.0.tar.gz >BatchQC.Rcheck\00install.out 2>&1 && cp BatchQC.Rcheck\00install.out BatchQC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BatchQC.buildbin-libdir --install="check:BatchQC-install.out" --force-multiarch --no-vignettes --timings BatchQC_1.4.0.tar.gz
StartedAt: 2017-08-15 22:08:54 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:13:02 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 248.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BatchQC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BatchQC.buildbin-libdir BatchQC.Rcheck && mkdir BatchQC.buildbin-libdir BatchQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BatchQC.buildbin-libdir BatchQC_1.4.0.tar.gz >BatchQC.Rcheck\00install.out 2>&1 && cp BatchQC.Rcheck\00install.out BatchQC-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BatchQC.buildbin-libdir --install="check:BatchQC-install.out" --force-multiarch --no-vignettes --timings BatchQC_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BatchQC.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 'BatchQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BatchQC' version '1.4.0'
* 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 'BatchQC' can be installed ... OK
* checking installed package size ... OK
* 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
gls.series.C: no visible global function definition for 'lm.fit'
Undefined global functions or variables:
  lm.fit
Consider adding
  importFrom("stats", "lm.fit")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'lmFitC'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
batchQC 5.38   0.31     6.1
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/BatchQC.Rcheck/00check.log'
for details.


BatchQC.Rcheck/00install.out:


install for i386

* installing *source* package 'BatchQC' ...
** R
** data
** 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 'BatchQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BatchQC' as BatchQC_1.4.0.zip
* DONE (BatchQC)

BatchQC.Rcheck/examples_i386/BatchQC-Ex.timings:

nameusersystemelapsed
batchQC3.930.284.61
batchQC_analyze0.300.020.31
batchQC_condition_adjusted0.060.000.07
batchQC_filter_genes0.080.000.07
batchQC_fsva_adjusted0.30.00.3
batchQC_num.sv0.090.000.10
batchQC_shapeVariation0.170.000.17
batchQC_sva0.210.000.20
batchQC_svregress_adjusted0.150.010.17
batchqc_circosplot0.170.000.17
batchqc_correlation0.180.000.18
batchqc_corscatter0.040.000.04
batchqc_explained_variation0.030.000.03
batchqc_heatmap0.110.000.11
batchqc_pc_explained_variation0.060.000.06
batchqc_pca0.020.020.03
batchqc_pca_svd0.120.000.13
batchtest0.060.000.06
combatPlot0.110.000.11
getShinyInput0.070.020.08
getShinyInputCombat000
getShinyInputOrig0.030.030.06
getShinyInputSVA000
getShinyInputSVAf000
getShinyInputSVAr000
gnormalize000
log2CPM0.030.010.05
rnaseq_sim0.120.030.15
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
setShinyInputSVA000
setShinyInputSVAf000
setShinyInputSVAr000

BatchQC.Rcheck/examples_x64/BatchQC-Ex.timings:

nameusersystemelapsed
batchQC5.380.316.10
batchQC_analyze0.40.00.4
batchQC_condition_adjusted0.030.020.05
batchQC_filter_genes0.090.000.09
batchQC_fsva_adjusted0.330.000.33
batchQC_num.sv0.090.000.09
batchQC_shapeVariation0.240.000.24
batchQC_sva0.20.00.2
batchQC_svregress_adjusted0.160.010.17
batchqc_circosplot0.230.000.24
batchqc_correlation0.190.000.19
batchqc_corscatter0.040.020.06
batchqc_explained_variation0.050.010.06
batchqc_heatmap0.160.000.16
batchqc_pc_explained_variation0.070.000.08
batchqc_pca0.020.020.03
batchqc_pca_svd0.190.000.19
batchtest0.060.000.06
combatPlot0.150.000.15
getShinyInput0.080.000.08
getShinyInputCombat000
getShinyInputOrig0.050.000.05
getShinyInputSVA000
getShinyInputSVAf000
getShinyInputSVAr000
gnormalize000
log2CPM0.030.000.03
rnaseq_sim0.160.010.18
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
setShinyInputSVA000
setShinyInputSVAf000
setShinyInputSVAr000