Multiple platform build/check report for BioC 3.12 - CHECK report for transite on tokay1

Package: transite

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transite.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings transite_1.8.0.tar.gz

StartedAt: 2021-05-06 07:39:39 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 07:54:19 -0400 (Thu, 06 May 2021)

EllapsedTime: 879.9 seconds

RetCode: 0

Status: OK

CheckDir: transite.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transite.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings transite_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/transite.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 'transite/DESCRIPTION' ... OK
* this is package 'transite' version '1.8.0'
* 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 'transite' can be installed ... OK
* 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 ... 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 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-3.12-bioc/R/library/transite/libs/i386/transite.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-3.12-bioc/R/library/transite/libs/x64/transite.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
run_kmer_tsma             58.53   0.00   62.05
run_kmer_spma             49.39   0.06   49.45
calculate_kmer_enrichment  5.69   0.00    5.69
run_matrix_spma            5.12   0.17    9.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
run_kmer_tsma             60.01   0.03   62.25
run_kmer_spma             50.92   0.01   52.72
calculate_kmer_enrichment  6.81   0.00    6.81
compute_kmer_enrichment    4.78   0.04    6.06
run_matrix_spma            3.07   0.11    5.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/transite.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/transite_1.8.0.tar.gz && rm -rf transite.buildbin-libdir && mkdir transite.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transite.buildbin-libdir transite_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL transite_1.8.0.zip && rm transite_1.8.0.tar.gz transite_1.8.0.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  597k  100  597k    0     0  23.5M      0 --:--:-- --:--:-- --:--:-- 24.3M

install for i386

* installing *source* package 'transite' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c scoring.cpp -o scoring.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o transite.dll tmp.def RcppExports.o scoring.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/transite.buildbin-libdir/00LOCK-transite/00new/transite/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'transite'
    finding HTML links ... done
    RBPMotif-class                          html  
    SpectrumScore-class                     html  
    calculate_kmer_enrichment               html  
    calculate_local_consistency             html  
    calculate_motif_enrichment              html  
    calculate_transcript_mc                 html  
    check_kmers                             html  
    classify_spectrum                       html  
    compute_kmer_enrichment                 html  
    count_homopolymer_corrected_kmers       html  
    create_kmer_motif                       html  
    create_matrix_motif                     html  
    draw_volcano_plot                       html  
    estimate_significance                   html  
    estimate_significance_core              html  
    ge                                      html  
    generate_iupac_by_kmers                 html  
    generate_iupac_by_matrix                html  
    generate_kmers                          html  
    generate_kmers_from_iupac               html  
    generate_permuted_enrichments           html  
    geometric_mean                          html  
    get_motif_by_id                         html  
    get_motif_by_rbp                        html  
    get_motifs                              html  
    get_motifs_meta_info                    html  
    get_ppm                                 html  
    init_iupac_lookup_table                 html  
    kmers_enrichment                        html  
    motifs                                  html  
    p_combine                               html  
    run_kmer_spma                           html  
    run_kmer_tsma                           html  
    run_matrix_spma                         html  
    run_matrix_tsma                         html  
    score_sequences                         html  
    score_spectrum                          html  
    score_transcripts                       html  
    score_transcripts_single_motif          html  
    set_motifs                              html  
    subdivide_data                          html  
    toy_motif_matrix                        html  
    transite                                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 'transite' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c scoring.cpp -o scoring.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o transite.dll tmp.def RcppExports.o scoring.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/transite.buildbin-libdir/transite/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transite' as transite_1.8.0.zip
* DONE (transite)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'transite' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(testthat)
> library(transite)
> 
> test_check("transite")
== Skipped tests ===============================================================
* multi-core not available on i386 (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 94 ]
> 
> proc.time()
   user  system elapsed 
  86.28    0.90  186.73


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(transite)
> 
> test_check("transite")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
 110.98    0.59  237.12

name	user	system	elapsed
RBPMotif-class	0	0	0
SpectrumScore-class	0	0	0
calculate_kmer_enrichment	5.69	0.00	5.69
calculate_local_consistency	0.45	0.12	0.58
calculate_motif_enrichment	1.62	0.06	1.69
calculate_transcript_mc	0	0	0
check_kmers	0	0	0
classify_spectrum	2.83	0.35	3.17
compute_kmer_enrichment	3.44	0.03	3.47
create_kmer_motif	0	0	0
create_matrix_motif	0.02	0.00	0.01
draw_volcano_plot	0.37	0.00	0.38
estimate_significance_core	0.02	0.00	0.01
generate_iupac_by_kmers	0	0	0
generate_iupac_by_matrix	0	0	0
generate_kmers	0.12	0.00	0.13
generate_kmers_from_iupac	0.02	0.00	0.02
geometric_mean	0	0	0
get_motif_by_id	0	0	0
get_motif_by_rbp	0	0	0
get_motifs	0	0	0
get_motifs_meta_info	0.01	0.00	0.01
get_ppm	0.02	0.00	0.02
init_iupac_lookup_table	0	0	0
p_combine	0	0	0
run_kmer_spma	49.39	0.06	49.45
run_kmer_tsma	58.53	0.00	62.05
run_matrix_spma	5.12	0.17	9.06
run_matrix_tsma	0.04	0.00	0.03
score_sequences	0.00	0.02	0.02
score_spectrum	3.70	0.00	3.71
score_transcripts	0.01	0.00	0.02
set_motifs	0	0	0
subdivide_data	0.02	0.00	0.02

name	user	system	elapsed
RBPMotif-class	0.02	0.00	0.02
SpectrumScore-class	0	0	0
calculate_kmer_enrichment	6.81	0.00	6.81
calculate_local_consistency	0.35	0.05	0.39
calculate_motif_enrichment	2.17	0.01	2.19
calculate_transcript_mc	0	0	0
check_kmers	0	0	0
classify_spectrum	2.99	0.14	3.16
compute_kmer_enrichment	4.78	0.04	6.06
create_kmer_motif	0.01	0.00	0.02
create_matrix_motif	0	0	0
draw_volcano_plot	0.46	0.01	0.47
estimate_significance_core	0	0	0
generate_iupac_by_kmers	0	0	0
generate_iupac_by_matrix	0	0	0
generate_kmers	0.26	0.00	0.27
generate_kmers_from_iupac	0	0	0
geometric_mean	0	0	0
get_motif_by_id	0.02	0.00	0.01
get_motif_by_rbp	0	0	0
get_motifs	0	0	0
get_motifs_meta_info	0.02	0.00	0.02
get_ppm	0.02	0.00	0.01
init_iupac_lookup_table	0	0	0
p_combine	0	0	0
run_kmer_spma	50.92	0.01	52.72
run_kmer_tsma	60.01	0.03	62.25
run_matrix_spma	3.07	0.11	5.84
run_matrix_tsma	0.01	0.00	0.02
score_sequences	0.02	0.00	0.02
score_spectrum	3.04	0.03	3.07
score_transcripts	0	0	0
set_motifs	0	0	0
subdivide_data	0	0	0

CHECK report for transite on tokay1

Summary

Command output

Installation output

Tests output

Example timings