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CHECK report for rfPred on tokay1

This page was generated on 2019-04-13 11:23:04 -0400 (Sat, 13 Apr 2019).

Package 1295/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rfPred 1.20.0
Hugo Varet
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/rfPred
Branch: RELEASE_3_8
Last Commit: 73789cf
Last Changed Date: 2018-10-30 11:41:51 -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: rfPred
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rfPred.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rfPred_1.20.0.tar.gz
StartedAt: 2019-04-13 04:59:21 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:02:23 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 182.5 seconds
RetCode: 0
Status:  OK  
CheckDir: rfPred.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:rfPred.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rfPred_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rfPred.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 'rfPred/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rfPred' version '1.20.0'
* 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 'rfPred' 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 ... NOTE
'library' or 'require' call to 'Rsamtools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'IRanges' 'Rsamtools' 'data.table' 'methods' 'parallel'
  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
rfPred_scores_motor: no visible global function definition for
  'as.data.table'
rfPred_scores_motor: no visible global function definition for
  'IRanges'
rfPred_scores_motor: no visible global function definition for
  'scanTabix'
rfPred_scores_motor: no visible global function definition for
  'TabixFile'
rfPred_scores_motor: no visible global function definition for
  'makeCluster'
rfPred_scores_motor: no visible global function definition for
  'parLapply'
rfPred_scores_motor: no visible global function definition for
  'clusterSplit'
rfPred_scores_motor : <anonymous>: no visible global function
  definition for 'scanTabix'
rfPred_scores_motor: no visible global function definition for
  'stopCluster'
rfPred_scores_motor: no visible global function definition for
  'write.csv2'
rfPred_scores,GRanges: no visible global function definition for
  'seqlevels<-'
rfPred_scores,GRanges: no visible global function definition for
  'seqlevels'
rfPred_scores,character: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  IRanges TabixFile as.data.table clusterSplit makeCluster parLapply
  read.table scanTabix seqlevels seqlevels<- stopCluster write.csv2
Consider adding
  importFrom("utils", "read.table", "write.csv2")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/rfPred/libs/i386/rfPred.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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-3.8-bioc/meat/rfPred.Rcheck/00check.log'
for details.



Installation output

rfPred.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/rfPred_1.20.0.tar.gz && rm -rf rfPred.buildbin-libdir && mkdir rfPred.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rfPred.buildbin-libdir rfPred_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rfPred_1.20.0.zip && rm rfPred_1.20.0.tar.gz rfPred_1.20.0.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  890k  100  890k    0     0  3871k      0 --:--:-- --:--:-- --:--:-- 3939k

install for i386

* installing *source* package 'rfPred' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c outstring.c -o outstring.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o rfPred.dll tmp.def outstring.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rfPred.buildbin-libdir/rfPred/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rfPred'
    finding HTML links ... done
    example_GRanges                         html  
    rfPred-package                          html  
    rfPred_scores-methods                   html  
    rfPred_scores_motor                     html  
    variant_list_Y                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rfPred' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c outstring.c -o outstring.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rfPred.dll tmp.def outstring.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/rfPred.buildbin-libdir/rfPred/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rfPred' as rfPred_1.20.0.zip
* DONE (rfPred)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rfPred' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

rfPred.Rcheck/examples_i386/rfPred-Ex.timings

nameusersystemelapsed
rfPred_scores-methods0.630.100.84

rfPred.Rcheck/examples_x64/rfPred-Ex.timings

nameusersystemelapsed
rfPred_scores-methods0.500.250.63