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CHECK report for RnaSeqSampleSize on tokay1

This page was generated on 2020-04-15 12:24:16 -0400 (Wed, 15 Apr 2020).

Package 1462/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnaSeqSampleSize 1.18.0
Shilin Zhao
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/RnaSeqSampleSize
Branch: RELEASE_3_10
Last Commit: def4537
Last Changed Date: 2019-10-29 13:09:08 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: RnaSeqSampleSize
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnaSeqSampleSize.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RnaSeqSampleSize_1.18.0.tar.gz
StartedAt: 2020-04-15 06:13:38 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:16:22 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 164.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: RnaSeqSampleSize.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnaSeqSampleSize.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RnaSeqSampleSize_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RnaSeqSampleSize.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RnaSeqSampleSize/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RnaSeqSampleSize' version '1.18.0'
* 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 'RnaSeqSampleSize' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'RnaSeqSampleSize' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RnaSeqSampleSize.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
convertIdOneToOne: no visible global function definition for
  'flush.console'
est_power_root: no visible global function definition for 'qnbinom'
est_power_root: no visible global function definition for 'pnbinom'
est_power_root: no visible global function definition for 'dnbinom'
generateModel: no visible global function definition for 'plot'
generateModel: no visible global function definition for 'points'
generateModel: no visible global function definition for 'polygon'
generateModel: no visible global function definition for 'rainbow'
generateModel: no visible global function definition for 'legend'
generateModel: no visible global function definition for 'lm'
generateModel: no visible global function definition for 'abline'
modelPower: no visible global function definition for 'qnbinom'
modelPower: no visible global function definition for 'pnbinom'
modelPower: no visible global function definition for 'dnbinom'
nb_pvalue_store: no visible global function definition for 'dnbinom'
pCutoffMatrix: no visible global function definition for 'qbeta'
plot_power_curve: no visible global function definition for 'plot'
plot_power_curve: no visible global function definition for 'legend'
plot_power_curve: no visible global function definition for 'abline'
plot_power_curve: no visible global function definition for 'lines'
sample_size: no visible global function definition for 'qnorm'
selectDistribution: no visible global function definition for 'data'
selectDistribution: no visible global function definition for 'is'
Undefined global functions or variables:
  abline data dnbinom flush.console is legend lines lm plot pnbinom
  points polygon qbeta qnbinom qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "polygon")
  importFrom("methods", "is")
  importFrom("stats", "dnbinom", "lm", "pnbinom", "qbeta", "qnbinom",
             "qnorm")
  importFrom("utils", "data", "flush.console")
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 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-3.10-bioc/R/library/RnaSeqSampleSize/libs/i386/RnaSeqSampleSize.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/RnaSeqSampleSize/libs/x64/RnaSeqSampleSize.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'RnaSeqSampleSize-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertIdOneToOne
> ### Title: convertId
> ### Aliases: convertIdOneToOne
> 
> ### ** Examples
> 
> x<-c("Q04837","P0C0L4","P0C0L5","O75379","Q13068","A2MYD1","P60709","P30462","P30475","P30479")
> convertIdOneToOne(x,filters="uniprotswissprot",verbose=TRUE)
Now conectting with ensembl. Internet acess is needed and it may use 30 seconds.
Error in getBM(attributes = attributes, filters = filters, values = x,  : 
  Invalid attribute(s): entrezgene 
Please use the function 'listAttributes' to get valid attribute names
Calls: convertIdOneToOne -> getBM
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RnaSeqSampleSize-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertIdOneToOne
> ### Title: convertId
> ### Aliases: convertIdOneToOne
> 
> ### ** Examples
> 
> x<-c("Q04837","P0C0L4","P0C0L5","O75379","Q13068","A2MYD1","P60709","P30462","P30475","P30479")
> convertIdOneToOne(x,filters="uniprotswissprot",verbose=TRUE)
Now conectting with ensembl. Internet acess is needed and it may use 30 seconds.
Error in getBM(attributes = attributes, filters = filters, values = x,  : 
  Invalid attribute(s): entrezgene 
Please use the function 'listAttributes' to get valid attribute names
Calls: convertIdOneToOne -> getBM
Execution halted
* 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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/RnaSeqSampleSize.Rcheck/00check.log'
for details.

Installation output

RnaSeqSampleSize.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/RnaSeqSampleSize_1.18.0.tar.gz && rm -rf RnaSeqSampleSize.buildbin-libdir && mkdir RnaSeqSampleSize.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnaSeqSampleSize.buildbin-libdir RnaSeqSampleSize_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL RnaSeqSampleSize_1.18.0.zip && rm RnaSeqSampleSize_1.18.0.tar.gz RnaSeqSampleSize_1.18.0.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  336k  100  336k    0     0  1326k      0 --:--:-- --:--:-- --:--:-- 1344k

install for i386

* installing *source* package 'RnaSeqSampleSize' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RnaSeqSampleSize.c -o RnaSeqSampleSize.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bd0.c -o bd0.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cumsumBorder.cpp -o cumsumBorder.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stirlerr.c -o stirlerr.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o RnaSeqSampleSize.dll tmp.def RcppExports.o RnaSeqSampleSize.o bd0.o cumsumBorder.o stirlerr.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/RnaSeqSampleSize.buildbin-libdir/00LOCK-RnaSeqSampleSize/00new/RnaSeqSampleSize/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RnaSeqSampleSize'
    finding HTML links ... done
    convertIdOneToOne                       html  
    est_count_dispersion                    html  
    est_power                               html  
    est_power_curve                         html  
    est_power_distribution                  html  
    optimize_parameter                      html  
    plot_power_curve                        html  
    sample_size                             html  
    sample_size_distribution                html  
** building package indices
** installing vignettes
   'RnaSeqSampleSize.Rnw' 
** testing if installed package can be loaded from temporary location
Warning: Package 'RnaSeqSampleSize' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'RnaSeqSampleSize' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RnaSeqSampleSize' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c RnaSeqSampleSize.c -o RnaSeqSampleSize.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bd0.c -o bd0.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cumsumBorder.cpp -o cumsumBorder.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stirlerr.c -o stirlerr.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o RnaSeqSampleSize.dll tmp.def RcppExports.o RnaSeqSampleSize.o bd0.o cumsumBorder.o stirlerr.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/RnaSeqSampleSize.buildbin-libdir/RnaSeqSampleSize/libs/x64
** testing if installed package can be loaded
Warning: Package 'RnaSeqSampleSize' is deprecated and will be removed from
  Bioconductor version 3.11
* MD5 sums
packaged installation of 'RnaSeqSampleSize' as RnaSeqSampleSize_1.18.0.zip
* DONE (RnaSeqSampleSize)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'RnaSeqSampleSize' successfully unpacked and MD5 sums checked

Tests output

Example timings

RnaSeqSampleSize.Rcheck/examples_i386/RnaSeqSampleSize-Ex.timings

nameusersystemelapsed

RnaSeqSampleSize.Rcheck/examples_x64/RnaSeqSampleSize-Ex.timings

nameusersystemelapsed