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CHECK report for biomvRCNS on tokay1

This page was generated on 2021-05-05 12:11:25 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the biomvRCNS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 181/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomvRCNS 1.30.0  (landing page)
Yang Du
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/biomvRCNS
Branch: RELEASE_3_12
Last Commit: 0cb8b43
Last Changed Date: 2020-10-27 10:49:21 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: biomvRCNS
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomvRCNS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biomvRCNS_1.30.0.tar.gz
StartedAt: 2021-05-05 00:55:42 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 01:03:43 -0400 (Wed, 05 May 2021)
EllapsedTime: 481.5 seconds
RetCode: 0
Status:   OK   
CheckDir: biomvRCNS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomvRCNS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biomvRCNS_1.30.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biomvRCNS.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biomvRCNS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biomvRCNS' version '1.30.0'
* 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 'biomvRCNS' 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' calls in package code:
  'GenomicFeatures' 'cluster' 'dynamicTreeCut' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biomvRGviz: no visible global function definition for 'rainbow'
biomvRGviz: no visible global function definition for 'hasArg'
biomvRGviz: no visible global function definition for 'graphics.off'
biomvRGviz: no visible global function definition for 'setEPS'
biomvRGviz: no visible global function definition for 'postscript'
biomvRGviz: no visible global function definition for 'pdf'
biomvRGviz: no visible global function definition for 'dev.off'
biomvRhsmm: no visible global function definition for 'is'
biomvRhsmm: no visible binding for global variable 'mclapply'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'DataFrame'
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for 'Rle'
biomvRhsmm: no visible global function definition for 'DataFrame'
biomvRhsmm: no visible binding for global variable 'DataFrame'
biomvRhsmm: no visible global function definition for 'new'
biomvRmgmr: no visible global function definition for 'seqlevels<-'
biomvRmgmr: no visible global function definition for 'DataFrame'
biomvRmgmr: no visible global function definition for 'new'
biomvRseg: no visible global function definition for 'seqlevels<-'
biomvRseg: no visible global function definition for 'DataFrame'
biomvRseg: no visible global function definition for 'new'
estEmis: no visible global function definition for 'clara'
gammaFit: no visible global function definition for 'cov.wt'
hsmmRun: no visible global function definition for 'Rle'
hsmmRun : <anonymous>: no visible global function definition for 'Rle'
hsmmRun: no visible global function definition for 'seqlevels<-'
initEmis : <anonymous>: no visible global function definition for
  'dpois'
initEmis : <anonymous>: no visible global function definition for
  'dnorm'
initEmis : <anonymous>: no visible global function definition for
  'dnbinom'
initEmis : <anonymous>: no visible global function definition for
  'cov2cor'
initEmis : <anonymous>: no visible global function definition for 'dt'
initEmis : <anonymous>: no visible global function definition for
  'cov.wt'
initEmis : <anonymous>: no visible global function definition for
  'weighted.mean'
initSojDd : <anonymous>: no visible global function definition for
  'dgamma'
initSojDd : <anonymous>: no visible global function definition for
  'dpois'
initSojDd : <anonymous>: no visible global function definition for
  'dnbinom'
maxGapminRun: no visible global function definition for 'Rle'
maxGapminRun: no visible global function definition for 'runValue'
nbinomCLLDD: no visible global function definition for 'cov.wt'
nbinomCLLDD: no visible global function definition for 'dnbinom'
poisFit : <anonymous>: no visible global function definition for
  'dpois'
preClustGrp: no visible global function definition for 'dist'
preClustGrp: no visible global function definition for 'hclust'
preClustGrp: no visible global function definition for 'cutreeDynamic'
regionSegAlphaNB: no visible global function definition for 'mclapply'
regionSegCost: no visible global function definition for 'mclapply'
simSegData: no visible global function definition for 'runValue'
simSegData: no visible global function definition for 'Rle'
simSegData: no visible global function definition for 'pdf'
simSegData: no visible global function definition for 'ts.plot'
simSegData: no visible global function definition for 'dev.off'
simUvSegData: no visible global function definition for 'rnorm'
simUvSegData: no visible global function definition for 'rt'
simUvSegData: no visible global function definition for 'rgamma'
simUvSegData: no visible global function definition for 'rpois'
simUvSegData: no visible global function definition for 'rnbinom'
sojournAnno: no visible global function definition for 'is'
sojournAnno: no visible global function definition for 'transcripts'
sojournAnno: no visible global function definition for 'seqlengths'
sojournAnno: no visible global function definition for 'exons'
sojournAnno: no visible global function definition for
  'intronsByTranscript'
splitFarNeighbouryhat: no visible global function definition for
  'runValue'
tmvtfFit: no visible global function definition for 'cov.wt'
unifMJ : <anonymous>: no visible global function definition for 'dunif'
unifMJ : <anonymous> : <anonymous>: no visible global function
  definition for 'dunif'
plot,biomvRCNS-ANY: no visible binding for global variable 'ssetst'
Undefined global functions or variables:
  DataFrame Rle clara cov.wt cov2cor cutreeDynamic dev.off dgamma dist
  dnbinom dnorm dpois dt dunif exons graphics.off hasArg hclust
  intronsByTranscript is mclapply new pdf postscript rainbow rgamma
  rnbinom rnorm rpois rt runValue seqlengths seqlevels<- setEPS ssetst
  transcripts ts.plot weighted.mean
Consider adding
  importFrom("grDevices", "dev.off", "graphics.off", "pdf", "postscript",
             "rainbow", "setEPS")
  importFrom("methods", "hasArg", "is", "new")
  importFrom("stats", "cov.wt", "cov2cor", "dgamma", "dist", "dnbinom",
             "dnorm", "dpois", "dt", "dunif", "hclust", "rgamma",
             "rnbinom", "rnorm", "rpois", "rt", "ts.plot",
             "weighted.mean")
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 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-3.12-bioc/R/library/biomvRCNS/libs/i386/biomvRCNS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/biomvRCNS/libs/x64/biomvRCNS.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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
biomvRhsmm 6.82   0.98     7.8
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
biomvRhsmm 8.19   0.31    8.50
biomvRGviz 5.84   0.08    5.92
biomvRseg  5.35   0.00    5.35
* 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-3.12-bioc/meat/biomvRCNS.Rcheck/00check.log'
for details.



Installation output

biomvRCNS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/biomvRCNS_1.30.0.tar.gz && rm -rf biomvRCNS.buildbin-libdir && mkdir biomvRCNS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biomvRCNS.buildbin-libdir biomvRCNS_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL biomvRCNS_1.30.0.zip && rm biomvRCNS_1.30.0.tar.gz biomvRCNS_1.30.0.zip
###
##############################################################################
##############################################################################


  % 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  113k  100  113k    0     0  4745k      0 --:--:-- --:--:-- --:--:-- 4955k

install for i386

* installing *source* package 'biomvRCNS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c biomvRCNS.c -o biomvRCNS.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o biomvRCNS.dll tmp.def biomvRCNS.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/biomvRCNS.buildbin-libdir/00LOCK-biomvRCNS/00new/biomvRCNS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biomvRCNS'
    finding HTML links ... done
    biomvRCNS-class                         html  
    biomvRGviz                              html  
    biomvRhsmm                              html  
    biomvRmgmr                              html  
    biomvRseg                               html  
    coriell                                 html  
    encodeTP53                              html  
    hsmmRun                                 html  
    maxGapminRun                            html  
    regionSegAlphaNB                        html  
    regionSegCost                           html  
    simSegData                              html  
    sojournAnno                             html  
    splitFarNeighbour                       html  
    variosm                                 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 'biomvRCNS' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c biomvRCNS.c -o biomvRCNS.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o biomvRCNS.dll tmp.def biomvRCNS.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/biomvRCNS.buildbin-libdir/biomvRCNS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomvRCNS' as biomvRCNS_1.30.0.zip
* DONE (biomvRCNS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'biomvRCNS' successfully unpacked and MD5 sums checked

Tests output


Example timings

biomvRCNS.Rcheck/examples_i386/biomvRCNS-Ex.timings

nameusersystemelapsed
biomvRCNS-class000
biomvRGviz4.190.114.30
biomvRhsmm6.820.987.80
biomvRmgmr0.40.00.4
biomvRseg3.520.023.54
hsmmRun0.090.000.09
maxGapminRun0.020.000.01
regionSegAlphaNB0.060.000.07
regionSegCost000
simSegData0.020.000.01
sojournAnno0.030.000.03
splitFarNeighbour000

biomvRCNS.Rcheck/examples_x64/biomvRCNS-Ex.timings

nameusersystemelapsed
biomvRCNS-class000
biomvRGviz5.840.085.92
biomvRhsmm8.190.318.50
biomvRmgmr0.460.000.46
biomvRseg5.350.005.35
hsmmRun0.170.000.17
maxGapminRun000
regionSegAlphaNB0.060.000.06
regionSegCost000
simSegData000
sojournAnno0.040.000.05
splitFarNeighbour0.020.000.01