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BioC 3.6: CHECK report for GenVisR on tokay1

This page was generated on 2017-08-16 13:35:39 -0400 (Wed, 16 Aug 2017).

Package 558/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.7.0
Zachary Skidmore
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenVisR
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenVisR
Version: 1.7.0
Command: rm -rf GenVisR.buildbin-libdir GenVisR.Rcheck && mkdir GenVisR.buildbin-libdir GenVisR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenVisR.buildbin-libdir GenVisR_1.7.0.tar.gz >GenVisR.Rcheck\00install.out 2>&1 && cp GenVisR.Rcheck\00install.out GenVisR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenVisR.buildbin-libdir --install="check:GenVisR-install.out" --force-multiarch --no-vignettes --timings GenVisR_1.7.0.tar.gz
StartedAt: 2017-08-15 23:47:41 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:55:07 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 446.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GenVisR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenVisR.buildbin-libdir GenVisR.Rcheck && mkdir GenVisR.buildbin-libdir GenVisR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenVisR.buildbin-libdir GenVisR_1.7.0.tar.gz >GenVisR.Rcheck\00install.out 2>&1 && cp GenVisR.Rcheck\00install.out GenVisR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenVisR.buildbin-libdir --install="check:GenVisR-install.out" --force-multiarch --no-vignettes --timings GenVisR_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenVisR.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 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.7.0'
* 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 'GenVisR' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
waterfall: warning in waterfall_align(genes = gene_plot, heatmap =
  heatmap, burden = burden_plot, clinical = clinical_plot, proportion =
  proportions_plot, section_heights = section_heights): partial
  argument match of 'proportion' to 'proportions'
waterfall: warning in waterfall_align(genes = gene_plot, heatmap =
  heatmap, burden = burden_plot, proportion = proportions_plot,
  section_heights = section_heights): partial argument match of
  'proportion' to 'proportions'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
genCov    6.19   0.40    6.59
lolliplot 2.88   0.18   11.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
genCov    6.03   0.27    6.30
cnFreq    6.05   0.02    6.06
lolliplot 2.79   0.08   11.75
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenVisR.Rcheck/00check.log'
for details.


GenVisR.Rcheck/00install.out:


install for i386

* installing *source* package 'GenVisR' ...
** 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 'GenVisR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenVisR' as GenVisR_1.7.0.zip
* DONE (GenVisR)

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

nameusersystemelapsed
TvTi2.670.052.72
cnFreq4.710.174.88
cnSpec3.410.053.46
cnView1.480.161.64
compIdent3.170.143.31
covBars0.750.000.75
genCov6.190.406.59
geneViz3.080.073.14
ideoView0.340.000.34
lohSpec3.360.173.53
lohView0.560.000.57
lolliplot 2.88 0.1811.36
waterfall0.920.000.92

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

nameusersystemelapsed
TvTi3.640.073.72
cnFreq6.050.026.06
cnSpec3.970.023.98
cnView1.810.141.95
compIdent3.730.113.84
covBars0.890.000.89
genCov6.030.276.30
geneViz3.390.063.45
ideoView0.420.000.42
lohSpec4.100.024.11
lohView0.680.000.69
lolliplot 2.79 0.0811.75
waterfall0.880.000.87