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CHECK report for PSEA on tokay2

This page was generated on 2019-10-16 12:31:15 -0400 (Wed, 16 Oct 2019).

Package 1271/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PSEA 1.18.0
Alexandre Kuhn
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PSEA
Branch: RELEASE_3_9
Last Commit: 1edb4a7
Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PSEA
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PSEA_1.18.0.tar.gz
StartedAt: 2019-10-16 06:12:22 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:13:30 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 67.9 seconds
RetCode: 0
Status:  OK  
CheckDir: PSEA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PSEA_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PSEA.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PSEA/DESCRIPTION' ... OK
* this is package 'PSEA' version '1.18.0'
* 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 'PSEA' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
crplot: no visible global function definition for 'residuals'
crplot: no visible global function definition for 'dev.new'
crplot: no visible global function definition for 'plot'
crplot: no visible global function definition for 'abline'
crplot: no visible global function definition for 'points'
lmfitst : : no visible global function definition for
  'lm.fit'
swlm: no visible global function definition for 'formula'
swlm: no visible global function definition for 'lm'
Undefined global functions or variables:
  abline dev.new formula lm lm.fit plot points residuals
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "formula", "lm", "lm.fit", "residuals")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/PSEA.Rcheck/00check.log'
for details.



Installation output

PSEA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PSEA_1.18.0.tar.gz && rm -rf PSEA.buildbin-libdir && mkdir PSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PSEA.buildbin-libdir PSEA_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PSEA_1.18.0.zip && rm PSEA_1.18.0.tar.gz PSEA_1.18.0.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 5847k  100 5847k    0     0  25.4M      0 --:--:-- --:--:-- --:--:-- 26.3M

install for i386

* installing *source* package 'PSEA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PSEA'
    finding HTML links ... done
    coefmat                                 html  
    crplot                                  html  
    em_quantvg                              html  
    expression                              html  
    expression_GSE19380                     html  
    fmm                                     html  
    groups                                  html  
    information                             html  
    lmfitst                                 html  
    marker                                  html  
    pvalmat                                 html  
    slt                                     html  
    swlm                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'PSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PSEA' as PSEA_1.18.0.zip
* DONE (PSEA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PSEA' successfully unpacked and MD5 sums checked

Tests output


Example timings

PSEA.Rcheck/examples_i386/PSEA-Ex.timings

nameusersystemelapsed
coefmat0.050.010.06
crplot0.060.020.08
em_quantvg0.020.000.02
fmm0.010.000.01
lmfitst0.020.000.02
marker0.010.000.01
pvalmat0.030.000.03
slt000
swlm0.040.020.05

PSEA.Rcheck/examples_x64/PSEA-Ex.timings

nameusersystemelapsed
coefmat0.060.020.08
crplot0.080.000.08
em_quantvg0.010.000.02
fmm0.020.000.01
lmfitst0.000.010.02
marker0.010.000.02
pvalmat0.050.000.04
slt000
swlm0.050.000.05