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BioC 3.5: CHECK report for GeneOverlap on tokay2

This page was generated on 2017-08-16 13:22:54 -0400 (Wed, 16 Aug 2017).

Package 517/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneOverlap 1.12.0
Li Shen, Mount Sinai
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/GeneOverlap
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneOverlap
Version: 1.12.0
Command: rm -rf GeneOverlap.buildbin-libdir GeneOverlap.Rcheck && mkdir GeneOverlap.buildbin-libdir GeneOverlap.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneOverlap.buildbin-libdir GeneOverlap_1.12.0.tar.gz >GeneOverlap.Rcheck\00install.out 2>&1 && cp GeneOverlap.Rcheck\00install.out GeneOverlap-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GeneOverlap.buildbin-libdir --install="check:GeneOverlap-install.out" --force-multiarch --no-vignettes --timings GeneOverlap_1.12.0.tar.gz
StartedAt: 2017-08-15 23:56:24 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:57:20 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 55.3 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneOverlap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneOverlap.buildbin-libdir GeneOverlap.Rcheck && mkdir GeneOverlap.buildbin-libdir GeneOverlap.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneOverlap.buildbin-libdir GeneOverlap_1.12.0.tar.gz >GeneOverlap.Rcheck\00install.out 2>&1 && cp GeneOverlap.Rcheck\00install.out GeneOverlap-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GeneOverlap.buildbin-libdir --install="check:GeneOverlap-install.out" --force-multiarch --no-vignettes --timings GeneOverlap_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneOverlap.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 'GeneOverlap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneOverlap' version '1.12.0'
* 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 'GeneOverlap' 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
drawHeatmap,GeneOverlapMatrix: no visible global function definition
  for 'p.adjust'
print,GeneOverlap: no visible global function definition for 'head'
testGeneOverlap,GeneOverlap: no visible global function definition for
  'setNames'
Undefined global functions or variables:
  head p.adjust setNames
Consider adding
  importFrom("stats", "p.adjust", "setNames")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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' ... NOTE
The following files look like leftovers/mistakes:
  'Rplots.pdf'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GeneOverlap.Rcheck/00check.log'
for details.


GeneOverlap.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneOverlap' ...
** 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 'GeneOverlap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneOverlap' as GeneOverlap_1.12.0.zip
* DONE (GeneOverlap)

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

nameusersystemelapsed
GeneOverlap0.190.000.19
GeneOverlapMatrix0.280.000.28
drawHeatmap1.460.041.50
getGenomeSize0.140.000.14
getList0.070.000.06
getReadonly0.080.000.08
getReadonlyMatrix0.550.010.57
gs.RNASeq0.080.000.08
hESC.ChIPSeq.list0.110.000.11
hESC.RNASeq.list0.070.000.08
newGOM0.410.000.41
newGeneOverlap0.090.000.09
testGeneOverlap0.070.000.06

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

nameusersystemelapsed
GeneOverlap0.200.030.24
GeneOverlapMatrix0.520.000.51
drawHeatmap1.880.021.89
getGenomeSize0.070.020.09
getList0.050.000.05
getReadonly0.030.000.03
getReadonlyMatrix0.310.010.33
gs.RNASeq0.040.000.03
hESC.ChIPSeq.list0.060.000.06
hESC.RNASeq.list0.050.000.05
newGOM0.250.000.25
newGeneOverlap0.040.000.05
testGeneOverlap0.050.000.05