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This page was generated on 2022-03-18 11:07:29 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for FastqCleaner on riesling1


To the developers/maintainers of the FastqCleaner package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FastqCleaner.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 629/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FastqCleaner 1.13.0  (landing page)
Leandro Roser
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/FastqCleaner
git_branch: master
git_last_commit: a573586
git_last_commit_date: 2021-10-26 12:45:04 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: FastqCleaner
Version: 1.13.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FastqCleaner.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FastqCleaner_1.13.0.tar.gz
StartedAt: 2022-03-17 19:04:25 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:07:25 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 180.0 seconds
RetCode: 0
Status:   OK  
CheckDir: FastqCleaner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FastqCleaner.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FastqCleaner_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/FastqCleaner.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FastqCleaner/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FastqCleaner' version '1.13.0'
* 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 ... NOTE
Found the following non-portable file paths:
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-11-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-12-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-13-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-14-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-7-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-8-1.png

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'FastqCleaner' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    application   4.2Mb
* 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
* 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 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/FastqCleaner/libs/x64/FastqCleaner.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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/FastqCleaner.Rcheck/00check.log'
for details.



Installation output

FastqCleaner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FastqCleaner
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'FastqCleaner' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cpp_GC_content.cpp -o cpp_GC_content.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cpp_base_content.cpp -o cpp_base_content.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I../inst/include/ -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cpp_which_true.cpp -o cpp_which_true.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FastqCleaner.dll tmp.def RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-FastqCleaner/00new/FastqCleaner/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FastqCleaner'
    finding HTML links ... done
    adapter_filter                          html  
    asc2int                                 html  
    check_encoding                          html  
    check_onclick_                          html  
    complex_filter                          html  
    create_cleanfunction_                   html  
    create_uniform_width                    html  
    fixed_filter                            html  
    inject_letter_random                    html  
    int2asc                                 html  
    isNaturalNumber                         html  
    launch_fqc                              html  
    length_filter                           html  
    matching                                html  
    messageFun_                             html  
    myPlot                                  html  
    n_filter                                html  
    outputClean_                            html  
    plotA                                   html  
    plotB                                   html  
    plotC                                   html  
    plotD                                   html  
    plotE                                   html  
    plotF                                   html  
    plotG                                   html  
    plotH                                   html  
    plotI                                   html  
    plotJ                                   html  
    plotObjects                             html  
    processingFunction_                     html  
    qmean_filter                            html  
    random_length                           html  
    random_qual                             html  
    random_seq                              html  
    seq_filter                              html  
    seq_names                               html  
    trim3q_filter                           html  
    unique_filter                           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
* DONE (FastqCleaner)
Making 'packages.html' ... done

Tests output

FastqCleaner.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(testthat)
> library(FastqCleaner)
> 
> test_check("FastqCleaner")
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]

== Skipped tests ===============================================================
* On CRAN (10)

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   8.15    0.73    8.85 

Example timings

FastqCleaner.Rcheck/FastqCleaner-Ex.timings

nameusersystemelapsed
adapter_filter0.340.030.37
check_encoding0.130.000.12
complex_filter0.310.020.33
fixed_filter0.250.030.28
inject_letter_random0.130.000.13
launch_fqc000
length_filter0.260.010.28
matching0.170.000.17
n_filter0.410.080.48
qmean_filter0.290.010.31
random_length0.010.000.02
random_qual0.020.000.02
random_seq0.020.000.01
seq_filter0.200.020.22
seq_names0.010.000.02
trim3q_filter0.220.030.25
unique_filter0.270.000.26