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CHECK report for ISoLDE on tokay2

This page was generated on 2020-10-17 11:56:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ISoLDE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 903/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISoLDE 1.16.0
Christelle Reynès
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ISoLDE
Branch: RELEASE_3_11
Last Commit: 6a71aea
Last Changed Date: 2020-04-27 14:55:49 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: ISoLDE
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISoLDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ISoLDE_1.16.0.tar.gz
StartedAt: 2020-10-17 05:23:18 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:24:10 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 51.7 seconds
RetCode: 1
Status:  ERROR  
CheckDir: ISoLDE.Rcheck
Warnings: NA

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:ISoLDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ISoLDE_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ISoLDE.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 'ISoLDE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ISoLDE' version '1.16.0'
* package encoding: UTF-8
* 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 'ISoLDE' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.11-bioc/R/library/ISoLDE/libs/i386/ISoLDE.dll':
  Found '_exit', possibly from '_exit' (C)
  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-3.11-bioc/R/library/ISoLDE/libs/x64/ISoLDE.dll':
  Found '_exit', possibly from '_exit' (C)
  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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'ISoLDE_result_on_example.pdf', 'vignette.Rnw', 'workflow.pdf'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/vignette.Rnw'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testsIsolde.R'
 ERROR
Running the tests in 'tests/testsIsolde.R' failed.
Last 13 lines of output:
  Done
  > normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
  Reading normalized input file...
  Done
  > target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
  Reading target file...
  Done
  > 
  > res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
  Filtering your data...
  Error in getStrainValues(target) : 
    ERROR: strain column must contain 2 (and only 2) different values. 
  Values found: 
  Calls: filterT -> getStrainValues
  Execution halted
** running tests for arch 'x64' ...
  Running 'testsIsolde.R'
 ERROR
Running the tests in 'tests/testsIsolde.R' failed.
Last 13 lines of output:
  Done
  > normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
  Reading normalized input file...
  Done
  > target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
  Reading target file...
  Done
  > 
  > res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
  Filtering your data...
  Error in getStrainValues(target) : 
    ERROR: strain column must contain 2 (and only 2) different values. 
  Values found: 
  Calls: filterT -> getStrainValues
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/ISoLDE.Rcheck/00check.log'
for details.

Installation output

ISoLDE.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/ISoLDE_1.16.0.tar.gz && rm -rf ISoLDE.buildbin-libdir && mkdir ISoLDE.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ISoLDE.buildbin-libdir ISoLDE_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ISoLDE_1.16.0.zip && rm ISoLDE_1.16.0.tar.gz ISoLDE_1.16.0.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 1257k  100 1257k    0     0  18.3M      0 --:--:-- --:--:-- --:--:-- 20.4M

install for i386

* installing *source* package 'ISoLDE' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Isolde.c -o Isolde.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o ISoLDE.dll tmp.def Isolde.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/ISoLDE.buildbin-libdir/00LOCK-ISoLDE/00new/ISoLDE/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ISoLDE'
    finding HTML links ... done
    ISoLDE-package                          html  
    filterT                                 html  
    filteredASRcounts                       html  
    isolde_test                             html  
    normASRcounts                           html  
    rawASRcounts                            html  
    readNormInput                           html  
    readRawInput                            html  
    readTarget                              html  
    target                                  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 'ISoLDE' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Isolde.c -o Isolde.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ISoLDE.dll tmp.def Isolde.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/ISoLDE.buildbin-libdir/ISoLDE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ISoLDE' as ISoLDE_1.16.0.zip
* DONE (ISoLDE)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ISoLDE' successfully unpacked and MD5 sums checked

Tests output

ISoLDE.Rcheck/tests_i386/testsIsolde.Rout.fail


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ISoLDE)
> 
> targetfile <- system.file("extdata", "target_file.txt", package = "ISoLDE")
> rawfile <- system.file("extdata", "rawASRcounts_file.txt", package = "ISoLDE")
> normfile <- system.file("extdata", "normASRcounts_file.txt", package = "ISoLDE")
> 
> rawASRcounts <- readRawInput(raw_file = rawfile, del = "tab", rownames = TRUE, colnames = TRUE)
Reading raw input file...
Done
> normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
Reading normalized input file...
Done
> target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
Reading target file...
Done
> 
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
Filtering your data...
Error in getStrainValues(target) : 
  ERROR: strain column must contain 2 (and only 2) different values. 
Values found: 
Calls: filterT -> getStrainValues
Execution halted

ISoLDE.Rcheck/tests_x64/testsIsolde.Rout.fail


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ISoLDE)
> 
> targetfile <- system.file("extdata", "target_file.txt", package = "ISoLDE")
> rawfile <- system.file("extdata", "rawASRcounts_file.txt", package = "ISoLDE")
> normfile <- system.file("extdata", "normASRcounts_file.txt", package = "ISoLDE")
> 
> rawASRcounts <- readRawInput(raw_file = rawfile, del = "tab", rownames = TRUE, colnames = TRUE)
Reading raw input file...
Done
> normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
Reading normalized input file...
Done
> target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
Reading target file...
Done
> 
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
Filtering your data...
Error in getStrainValues(target) : 
  ERROR: strain column must contain 2 (and only 2) different values. 
Values found: 
Calls: filterT -> getStrainValues
Execution halted

Example timings

ISoLDE.Rcheck/examples_i386/ISoLDE-Ex.timings

nameusersystemelapsed
filterT0.370.020.39
filteredASRcounts0.030.000.04
isolde_test2.140.012.16
normASRcounts0.700.000.93
rawASRcounts0.190.000.20
readNormInput0.460.000.47
readRawInput0.110.000.11
readTarget0.070.000.06

ISoLDE.Rcheck/examples_x64/ISoLDE-Ex.timings

nameusersystemelapsed
filterT0.390.000.39
filteredASRcounts0.020.010.03
isolde_test1.850.021.86
normASRcounts0.610.030.64
rawASRcounts0.090.030.12
readNormInput0.360.020.38
readRawInput0.080.000.08
readTarget0.050.000.04