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CHECK report for PANR on tokay2

This page was generated on 2020-10-17 11:57:21 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE PANR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1263/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.34.0
Xin Wang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/PANR
Branch: RELEASE_3_11
Last Commit: 2711f73
Last Changed Date: 2020-04-27 14:26:47 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PANR
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PANR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PANR_1.34.0.tar.gz
StartedAt: 2020-10-17 06:44:01 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:45:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 104.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: PANR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PANR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PANR_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/PANR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.34.0'
* 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-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:21: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:85: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:85: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:89: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:89: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:9: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:44: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/data-Bakal2007.Rd:29: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/exportPAN.Rd:8: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/exportPAN.Rd:8: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/exportPAN.Rd:31: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/fitBM.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/fitNULL.Rd:25: file link 'dbeta' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/permNULL.Rd:28: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewNestedModules.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewNestedModules.Rd:38: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:10: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:28: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:42: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:60: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-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
* 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
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
fitNULL 25.67   0.27   25.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
fitNULL 24.77   0.14   25.06
* 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-3.11-bioc/meat/PANR.Rcheck/00check.log'
for details.

Installation output

PANR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/PANR_1.34.0.tar.gz && rm -rf PANR.buildbin-libdir && mkdir PANR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PANR.buildbin-libdir PANR_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL PANR_1.34.0.zip && rm PANR_1.34.0.tar.gz PANR_1.34.0.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 2027k  100 2027k    0     0  24.1M      0 --:--:-- --:--:-- --:--:-- 26.3M

install for i386

* installing *source* package 'PANR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:21: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:85: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:85: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:89: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/PAN-class.Rd:89: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
    SNR2p                                   html  
    assoScore                               html  
    buildPAN                                html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:9: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/buildPAN.Rd:44: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    cosineSim                               html  
    data-Bakal2007                          html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/data-Bakal2007.Rd:29: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    edgeWeight                              html  
    exportPAN                               html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/exportPAN.Rd:8: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/exportPAN.Rd:8: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/exportPAN.Rd:31: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
    fitBM                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/fitBM.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    fitNULL                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/fitNULL.Rd:25: file link 'dbeta' in package 'stats' does not exist and so has been treated as a topic
    infer                                   html  
    p2SNR                                   html  
    permNULL                                html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/permNULL.Rd:28: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    pvclustModule                           html  
    sigModules                              html  
    summarize                               html  
    view                                    html  
    viewLegend                              html  
    viewNestedModules                       html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewNestedModules.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewNestedModules.Rd:38: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
    viewPAN                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:10: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:28: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:42: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpygJIze/R.INSTALLbd828f318ee/PANR/man/viewPAN.Rd:60: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
** 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 'PANR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PANR' as PANR_1.34.0.zip
* DONE (PANR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'PANR' successfully unpacked and MD5 sums checked

Tests output

Example timings

PANR.Rcheck/examples_i386/PANR-Ex.timings

nameusersystemelapsed
BetaMixture-class000
PAN-class0.010.000.02
SNR2p000
assoScore0.020.000.01
buildPAN0.360.050.41
cosineSim0.020.000.02
data-Bakal20070.010.000.01
exportPAN000
fitBM000
fitNULL25.67 0.2725.95
infer0.360.000.36
p2SNR000
permNULL0.020.000.02
pvclustModule000
sigModules000
summarize0.060.000.06
view0.220.040.27
viewLegend000
viewNestedModules000
viewPAN000

PANR.Rcheck/examples_x64/PANR-Ex.timings

nameusersystemelapsed
BetaMixture-class000
PAN-class000
SNR2p000
assoScore000
buildPAN0.550.070.61
cosineSim000
data-Bakal20070.030.000.03
exportPAN000
fitBM0.010.000.02
fitNULL24.77 0.1425.06
infer0.470.000.47
p2SNR000
permNULL0.030.000.03
pvclustModule000
sigModules000
summarize0.060.000.06
view0.170.060.24
viewLegend000
viewNestedModules000
viewPAN000