Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQRSTUVWX[Y]Z

INSTALL report for YAPSA on tokay1

This page was generated on 2019-04-13 11:27:02 -0400 (Sat, 13 Apr 2019).

Package 1644/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.8.0
Daniel Huebschmann
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/YAPSA
Branch: RELEASE_3_8
Last Commit: 402f3f7
Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: YAPSA
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/YAPSA_1.8.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.8.0.zip && rm YAPSA_1.8.0.tar.gz YAPSA_1.8.0.zip
StartedAt: 2019-04-12 20:29:54 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 20:31:34 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 100.5 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/YAPSA_1.8.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.8.0.zip && rm YAPSA_1.8.0.tar.gz YAPSA_1.8.0.zip
###
##############################################################################
##############################################################################


  % 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 1078k  100 1078k    0     0  21.1M      0 --:--:-- --:--:-- --:--:-- 22.8M

install for i386

* installing *source* package 'YAPSA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'YAPSA'
    finding HTML links ... done
    LCD                                     html  
    LCD_complex_cutoff                      html  
    YAPSA                                   html  
    add_annotation                          html  
    add_as_fist_to_list                     html  
    aggregate_exposures_by_category         html  
    annotate_intermut_dist_PID              html  
    annotate_intermut_dist_cohort           html  
    annotation_exposures_barplot            html  
    annotation_heatmap_exposures            html  
    attribute_nucleotide_exchanges          html  
    build_gene_list_for_pathway             html  
    compare_SMCs                            html  
    compare_exposures                       html  
    compare_sets                            html  
    compare_to_catalogues                   html  
    complex_heatmap_exposures               html  
    compute_comparison_stat_df              html  
    cosineDist                              html  
    create_mutation_catalogue_from_VR       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_VR.Rd:49: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_VR.Rd:51: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_VR.Rd:18: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_VR.Rd:22: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_VR.Rd:86: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_VR.Rd:88: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
    create_mutation_catalogue_from_df       html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_df.Rd:39: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/create_mutation_catalogue_from_df.Rd:43: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
    cut_breaks_as_intervals                 html  
    cutoffs                                 html  
    exampleYAPSA                            html  
    exchange_colour_vector                  html  
    exposures_barplot                       html  
    extract_names_from_gene_list            html  
    find_affected_PIDs                      html  
    get_extreme_PIDs                        html  
    hclust_exposures                        html  
    makeVRangesFromDataFrame                html  
    make_catalogue_strata_df                html  
    make_comparison_matrix                  html  
    make_strata_df                          html  
    make_subgroups_df                       html  
    melt_exposures                          html  
    merge_exposures                         html  
    normalizeMotifs_otherRownames           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/normalizeMotifs_otherRownames.Rd:20: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/normalizeMotifs_otherRownames.Rd:22: file link 'SomaticSignatures' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/normalizeMotifs_otherRownames.Rd:10: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/normalizeMotifs_otherRownames.Rd:15: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
    normalize_df_per_dim                    html  
    plotExchangeSpectra                     html  
    plot_SMC                                html  
    plot_exposures                          html  
    plot_strata                             html  
    repeat_df                               html  
    run_SMC                                 html  
    run_annotate_vcf_pl                     html  
    run_comparison_catalogues               html  
    run_comparison_general                  html  
    run_kmer_frequency_correction           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_correction.Rd:40: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_correction.Rd:51: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_correction.Rd:52: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_correction.Rd:62: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
    run_kmer_frequency_normalization        html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_normalization.Rd:29: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_normalization.Rd:40: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_normalization.Rd:41: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/run_kmer_frequency_normalization.Rd:51: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
    run_plot_strata_general                 html  
    shapiro_if_possible                     html  
    sigs                                    html  
    split_exposures_by_subgroups            html  
    stat_plot_subgroups                     html  
    stat_test_SMC                           html  
    stat_test_subgroups                     html  
    stderrmean                              html  
    sum_over_list_of_df                     html  
    targetCapture_cor_factors               html  
    test_exposureAffected                   html  
    test_gene_list_in_exposures             html  
    transform_rownames_R_to_MATLAB          html  
    translate_to_hg19                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpaa1Fr2/R.INSTALL24ac21ea1e73/YAPSA/man/translate_to_hg19.Rd:31: file link 'BSgenome.Hsapiens.UCSC.hg19' in package 'BSgenome.Hsapiens.UCSC.hg19' does not exist and so has been treated as a topic
    trellis_rainfall_plot                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'YAPSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.8.0.zip
* DONE (YAPSA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked
In R CMD INSTALL