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CHECK report for NormqPCR on tokay1

This page was generated on 2021-05-06 12:32:33 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the NormqPCR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1233/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.36.0  (landing page)
James Perkins
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/NormqPCR
Branch: RELEASE_3_12
Last Commit: 3d0cc46
Last Changed Date: 2020-10-27 10:42:19 -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    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: NormqPCR
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings NormqPCR_1.36.0.tar.gz
StartedAt: 2021-05-06 05:07:27 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:10:43 -0400 (Thu, 06 May 2021)
EllapsedTime: 196.1 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: NormqPCR.Rcheck
Warnings: 1

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:NormqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings NormqPCR_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/NormqPCR.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 'NormqPCR/DESCRIPTION' ... OK
* this is package 'NormqPCR' version '1.36.0'
* 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 'NormqPCR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6ZjOOZ/R.INSTALLb5865301ed0/NormqPCR/man/ComputeNRQs.Rd:14: file link 'qPCRBatch' in package 'ReadqPCR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6ZjOOZ/R.INSTALLb5865301ed0/NormqPCR/man/CqValues.Rd:23: file link 'CyclesSet' in package 'ReadqPCR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/NormqPCR.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
CqValues,CyclesSet: no visible binding for global variable 'l5'
Undefined global functions or variables:
  l5
* 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 (user + system) or elapsed time > 5s
          user system elapsed
CqValues 42.55   0.17   43.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
CqValues 54.89   0.11      55
* 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-3.12-bioc/meat/NormqPCR.Rcheck/00check.log'
for details.



Installation output

NormqPCR.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/NormqPCR_1.36.0.tar.gz && rm -rf NormqPCR.buildbin-libdir && mkdir NormqPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NormqPCR.buildbin-libdir NormqPCR_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL NormqPCR_1.36.0.zip && rm NormqPCR_1.36.0.tar.gz NormqPCR_1.36.0.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  310k  100  310k    0     0  11.0M      0 --:--:-- --:--:-- --:--:-- 11.6M

install for i386

* installing *source* package 'NormqPCR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NormqPCR'
    finding HTML links ... done
    Bladder                                 html  
    BladderRepro                            html  
    Colon                                   html  
    ComputeNRQs                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6ZjOOZ/R.INSTALLb5865301ed0/NormqPCR/man/ComputeNRQs.Rd:14: file link 'qPCRBatch' in package 'ReadqPCR' does not exist and so has been treated as a topic
    CqValues                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6ZjOOZ/R.INSTALLb5865301ed0/NormqPCR/man/CqValues.Rd:23: file link 'CyclesSet' in package 'ReadqPCR' does not exist and so has been treated as a topic
    NormqPCR-package                        html  
    combineTechReps                         html  
    combineTechRepsSD                       html  
    deltaCt                                 html  
    deltaDeltaCt                            html  
    geNorm                                  html  
    geomMean                                html  
    makeAllNAs                              html  
    makeAllNewVal                           html  
    replaceAboveCutOff                      html  
    replaceNAs                              html  
    selectHKs                               html  
    stabMeasureM                            html  
    stabMeasureRho                          html  
** building package indices
** installing vignettes
   'NormqPCR.Rnw' 
** 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 'NormqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormqPCR' as NormqPCR_1.36.0.zip
* DONE (NormqPCR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'NormqPCR' successfully unpacked and MD5 sums checked

Tests output


Example timings

NormqPCR.Rcheck/examples_i386/NormqPCR-Ex.timings

nameusersystemelapsed
Bladder0.050.000.05
BladderRepro0.010.000.01
Colon0.000.020.01
ComputeNRQs0.150.010.24
CqValues42.55 0.1743.11
NormqPCR-package000
combineTechReps0.050.000.04
combineTechRepsSD0.060.000.07
deltaCt0.080.000.09
deltaDeltaCt0.080.000.08
geNorm0.010.000.01
geomMean000
makeAllNAs0.080.000.08
makeAllNewVal0.080.000.08
replaceAboveCutOff0.080.000.08
replaceNAs0.110.000.11
selectHKs0.030.000.03
stabMeasureM0.140.000.14
stabMeasureRho0.150.000.15

NormqPCR.Rcheck/examples_x64/NormqPCR-Ex.timings

nameusersystemelapsed
Bladder0.020.000.01
BladderRepro000
Colon0.010.000.02
ComputeNRQs0.300.010.31
CqValues54.89 0.1155.00
NormqPCR-package000
combineTechReps0.070.000.07
combineTechRepsSD0.150.000.14
deltaCt0.120.000.13
deltaDeltaCt0.160.000.16
geNorm0.000.020.01
geomMean000
makeAllNAs0.070.000.08
makeAllNewVal0.110.000.11
replaceAboveCutOff0.080.000.08
replaceNAs0.080.000.08
selectHKs0.030.000.03
stabMeasureM0.110.010.12
stabMeasureRho0.070.020.09