Daniel Huebschmann
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/YAPSA |
| Branch: RELEASE_3_9 |
| Last Commit: 06af18e |
| Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:36:36 -0400 (Wed, 16 Oct 2019).
| Package 1736/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| YAPSA 1.10.0 Daniel Huebschmann
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: YAPSA |
| Version: 1.10.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/YAPSA_1.10.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.10.0.zip && rm YAPSA_1.10.0.tar.gz YAPSA_1.10.0.zip |
| StartedAt: 2019-10-15 21:05:26 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 21:07:30 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 124.3 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/YAPSA_1.10.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.10.0.zip && rm YAPSA_1.10.0.tar.gz YAPSA_1.10.0.zip
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install for i386
* installing *source* package 'YAPSA' ...
** using staged installation
** 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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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-3.9-bioc/tmpdir/RtmpAFMFZ2/R.INSTALL2a2c114f64a6/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 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 'YAPSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.10.0.zip
* DONE (YAPSA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked