Back to Multiple platform build/check report for BioC 3.6
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for PANR on tokay1

This page was generated on 2018-04-12 13:21:10 -0400 (Thu, 12 Apr 2018).

Package 997/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.24.0
Xin Wang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PANR
Branch: RELEASE_3_6
Last Commit: 6b27f5b
Last Changed Date: 2017-10-30 12:39:35 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PANR
Version: 1.24.0
Command: rm -rf PANR.buildbin-libdir PANR.Rcheck && mkdir PANR.buildbin-libdir PANR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.24.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.24.0.tar.gz
StartedAt: 2018-04-12 01:59:49 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:01:34 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 104.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: PANR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PANR.buildbin-libdir PANR.Rcheck && mkdir PANR.buildbin-libdir PANR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PANR.buildbin-libdir PANR_1.24.0.tar.gz >PANR.Rcheck\00install.out 2>&1 && cp PANR.Rcheck\00install.out PANR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=PANR.buildbin-libdir --install="check:PANR-install.out" --force-multiarch --no-vignettes --timings PANR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PANR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PANR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PANR' version '1.24.0'
* 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 'PANR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:21: missing file link 'BetaMixture'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:85: missing file link 'igraph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:85: missing file link 'RedeR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:89: missing file link 'igraph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:89: missing file link 'RedeR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:9: missing file link 'igraph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:9: missing file link 'RedeR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:40: missing file link 'BetaMixture'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:44: missing file link 'BetaMixture'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/data-Bakal2007.Rd:29: missing file link 'BetaMixture'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/exportPAN.Rd:8: missing file link 'write.graph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/exportPAN.Rd:8: missing file link 'igraph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/exportPAN.Rd:31: missing file link 'write.graph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/fitBM.Rd:40: missing file link 'BetaMixture'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/fitNULL.Rd:25: missing file link 'dbeta'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/permNULL.Rd:28: missing file link 'BetaMixture'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewNestedModules.Rd:9: missing file link 'RedeR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewNestedModules.Rd:38: missing file link 'RedeR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:10: missing file link 'RedeR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:28: missing file link 'layout'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:42: missing file link 'RedeR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:60: missing file link 'layout'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/PANR.Rcheck/00install.out' for details.
* 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
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for 'runif'
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for 'pbeta'
p2SNR,BetaMixture-numeric_Or_integer: no visible global function
  definition for 'qbeta'
Undefined global functions or variables:
  pbeta qbeta runif
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif")
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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitNULL 29.38   0.11   29.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
fitNULL 25.33   0.18    25.5
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/PANR.Rcheck/00check.log'
for details.

Installation output

PANR.Rcheck/00install.out


install for i386

* installing *source* package 'PANR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'PANR'
    finding HTML links ... done
    BetaMixture-class                       html  
    PAN-class                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:21: missing file link 'BetaMixture'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:85: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:85: missing file link 'RedeR'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:89: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/PAN-class.Rd:89: missing file link 'RedeR'
    SNR2p                                   html  
    assoScore                               html  
    buildPAN                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:9: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:9: missing file link 'RedeR'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:40: missing file link 'BetaMixture'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/buildPAN.Rd:44: missing file link 'BetaMixture'
    cosineSim                               html  
    data-Bakal2007                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/data-Bakal2007.Rd:29: missing file link 'BetaMixture'
    edgeWeight                              html  
    exportPAN                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/exportPAN.Rd:8: missing file link 'write.graph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/exportPAN.Rd:8: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/exportPAN.Rd:31: missing file link 'write.graph'
    fitBM                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/fitBM.Rd:40: missing file link 'BetaMixture'
    fitNULL                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/fitNULL.Rd:25: missing file link 'dbeta'
    infer                                   html  
    p2SNR                                   html  
    permNULL                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/permNULL.Rd:28: missing file link 'BetaMixture'
    pvclustModule                           html  
    sigModules                              html  
    summarize                               html  
    view                                    html  
    viewLegend                              html  
    viewNestedModules                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewNestedModules.Rd:9: missing file link 'RedeR'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewNestedModules.Rd:38: missing file link 'RedeR'
    viewPAN                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:10: missing file link 'RedeR'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:28: missing file link 'layout'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:42: missing file link 'RedeR'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpwlb8rs/R.INSTALL36b44f5c701/PANR/man/viewPAN.Rd:60: missing file link 'layout'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PANR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PANR' as PANR_1.24.0.zip
* DONE (PANR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

PANR.Rcheck/examples_i386/PANR-Ex.timings

nameusersystemelapsed
BetaMixture-class000
PAN-class000
SNR2p000
assoScore000
buildPAN0.740.030.77
cosineSim000
data-Bakal20070.010.000.01
exportPAN0.020.000.02
fitBM000
fitNULL29.38 0.1129.67
infer0.510.000.52
p2SNR000
permNULL0.020.010.04
pvclustModule000
sigModules000
summarize0.040.000.05
view0.410.020.51
viewLegend000
viewNestedModules000
viewPAN000

PANR.Rcheck/examples_x64/PANR-Ex.timings

nameusersystemelapsed
BetaMixture-class0.020.000.01
PAN-class000
SNR2p000
assoScore0.020.000.01
buildPAN0.920.010.94
cosineSim000
data-Bakal20070.030.000.03
exportPAN000
fitBM000
fitNULL25.33 0.1825.50
infer0.360.000.36
p2SNR000
permNULL0.010.000.02
pvclustModule000
sigModules000
summarize0.030.000.03
view0.410.000.41
viewLegend000
viewNestedModules000
viewPAN000