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CHECK report for PGSEA on tokay1

This page was generated on 2019-04-13 11:20:11 -0400 (Sat, 13 Apr 2019).

Package 1147/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PGSEA 1.56.0
Karl Dykema
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/PGSEA
Branch: RELEASE_3_8
Last Commit: 1ee369f
Last Changed Date: 2018-10-30 11:41:43 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PGSEA
Version: 1.56.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PGSEA_1.56.0.tar.gz
StartedAt: 2019-04-13 04:30:40 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:34:39 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 239.3 seconds
RetCode: 0
Status:  OK  
CheckDir: PGSEA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PGSEA_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/PGSEA.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 'PGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGSEA' version '1.56.0'
* 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 'PGSEA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'GO.db' 'KEGG.db'
  Please remove these calls from your code.
'library' or 'require' call to 'org.Hs.eg.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'GO.db' 'KEGG.db' 'annaffy' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aggregateExprs: warning in mget(ids, env = Env, ifnotfound = NA):
  partial argument match of 'env' to 'envir'
PGSEA: no visible global function definition for 'is'
PGSEA: no visible binding for global variable 't.test'
PGSEA: no visible binding for global variable 'sd'
PGSEA: no visible global function definition for 'pnorm'
aggregateExprs: no visible global function definition for 'is'
aggregateExprs: no visible global function definition for 'aggregate'
convertSmc: no visible global function definition for 'read.delim'
go2smc: no visible binding for global variable 'GOTERM'
go2smc: no visible binding for global variable 'org.Hs.egGO2ALLEGS'
go2smc: no visible global function definition for 'new'
kegg2smc: no visible binding for global variable 'KEGGPATHNAME2ID'
kegg2smc: no visible binding for global variable 'KEGGPATHID2EXTID'
kegg2smc: no visible global function definition for 'new'
readGmt: no visible global function definition for 'new'
readSmc: no visible global function definition for 'new'
smcPlot: no visible global function definition for 'par'
smcPlot: no visible global function definition for 'hclust'
smcPlot: no visible global function definition for 'dist'
smcPlot: no visible global function definition for 'image'
smcPlot: no visible global function definition for 'grid'
smcPlot: no visible global function definition for 'axis'
smcPlot: no visible global function definition for 'abline'
smcPlot: no visible global function definition for 'box'
writeSmc: no visible global function definition for 'write.table'
Undefined global functions or variables:
  GOTERM KEGGPATHID2EXTID KEGGPATHNAME2ID abline aggregate axis box
  dist grid hclust image is new org.Hs.egGO2ALLEGS par pnorm read.delim
  sd t.test write.table
Consider adding
  importFrom("graphics", "abline", "axis", "box", "grid", "image", "par")
  importFrom("methods", "is", "new")
  importFrom("stats", "aggregate", "dist", "hclust", "pnorm", "sd",
             "t.test")
  importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
go2smc 33.33   3.82   37.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
go2smc 36.14   1.04   37.19
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/PGSEA.Rcheck/00check.log'
for details.



Installation output

PGSEA.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/PGSEA_1.56.0.tar.gz && rm -rf PGSEA.buildbin-libdir && mkdir PGSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PGSEA.buildbin-libdir PGSEA_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL PGSEA_1.56.0.zip && rm PGSEA_1.56.0.tar.gz PGSEA_1.56.0.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  957k  100  957k    0     0  17.6M      0 --:--:-- --:--:-- --:--:-- 19.0M

install for i386

* installing *source* package 'PGSEA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PGSEA'
    finding HTML links ... done
    GOLUBmcs                                html  
    PGSEA                                   html  
    VAIgsc                                  html  
    VAImcs                                  html  
    aggregateExprs                          html  
    convertSmc                              html  
    editSmc                                 html  
    go2smc                                  html  
    kegg2smc                                html  
    nbEset                                  html  
    readGmt                                 html  
    readSmc                                 html  
    scanSmc                                 html  
    smcPlot                                 html  
    writeGmt                                html  
    writeSmc                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PGSEA' as PGSEA_1.56.0.zip
* DONE (PGSEA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'PGSEA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

PGSEA.Rcheck/examples_i386/PGSEA-Ex.timings

nameusersystemelapsed
GOLUBmcs0.070.010.10
PGSEA0.390.030.42
VAIgsc0.660.080.74
VAImcs0.260.000.26
aggregateExprs0.220.030.25
convertSmc000
editSmc0.010.000.01
go2smc33.33 3.8237.16
kegg2smc0.280.000.28
nbEset0.130.000.13
readGmt0.040.000.04
readSmc0.020.010.03
scanSmc0.010.000.02
smcPlot0.350.020.36
writeGmt0.040.000.05
writeSmc0.050.000.04

PGSEA.Rcheck/examples_x64/PGSEA-Ex.timings

nameusersystemelapsed
GOLUBmcs0.070.010.09
PGSEA0.440.000.44
VAIgsc0.640.030.68
VAImcs0.280.000.28
aggregateExprs0.210.030.24
convertSmc000
editSmc0.030.000.03
go2smc36.14 1.0437.19
kegg2smc0.230.030.27
nbEset0.090.000.09
readGmt0.030.000.03
readSmc0.050.000.04
scanSmc0.010.000.02
smcPlot0.350.010.36
writeGmt0.040.000.05
writeSmc0.050.000.04