Daniel Huebschmann
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/YAPSA |
| Branch: RELEASE_3_11 |
| Last Commit: 2e86384 |
| Last Changed Date: 2020-04-27 15:01:09 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:00 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE YAPSA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1900/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| YAPSA 1.14.0 Daniel Huebschmann
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: YAPSA |
| Version: 1.14.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/YAPSA_1.14.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.14.0.zip && rm YAPSA_1.14.0.tar.gz YAPSA_1.14.0.zip |
| StartedAt: 2020-10-16 19:35:39 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 19:37:36 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 117.3 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/3.11/bioc/src/contrib/YAPSA_1.14.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.14.0.zip && rm YAPSA_1.14.0.tar.gz YAPSA_1.14.0.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
GenomeOfNl_raw html
LCD html
LCD_SMC html
LCD_complex_cutoff html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:169: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:172: file link 'LCD_complex_cutoff_consensus' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:173: file link 'LCD_complex_cutoff_combined' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:174: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:177: file link 'LCD_complex_cutoff_combined' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:179: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:180: file link 'LCD_complex_cutoff_consensus' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:104: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
MutCat_indel_df html
SMC html
SMC_perPID 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
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/annotation_exposures_barplot.Rd:56: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
annotation_exposures_list_barplot html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/annotation_exposures_list_barplot.Rd:59: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
annotation_heatmap_exposures html
attribute_nucleotide_exchanges html
attribute_sequence_contex_indel html
attribution_of_indels html
build_gene_list_for_pathway html
classify_indels html
compare_SMCs html
compare_exposures html
compare_expousre_sets html
compare_sets html
compare_to_catalogues html
complex_heatmap_exposures html
computeLogLik html
compute_comparison_stat_df html
confIntExp html
confidence_indel_calulation html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/confidence_indel_calulation.Rd:40: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
confidence_indel_only_calulation html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/confidence_indel_only_calulation.Rd:32: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
correct_rounded html
cosineDist html
cosineMatchDist html
create_indel_mut_cat_from_df html
create_indel_mutation_catalogue_from_df
html
create_mutation_catalogue_from_VR html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:50: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:52: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:25: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:29: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:87: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:89: 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-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_df.Rd:50: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_df.Rd:54: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
cut_breaks_as_intervals html
cutoffs html
cutoffs_pcawg html
deriveSigInd_df html
disambiguateVector html
enrichSigs html
exampleINDEL_YAPSA html
exampleYAPSA html
exchange_colour_vector html
exome_mutCatRaw_df html
exposures_barplot html
extract_names_from_gene_list html
find_affected_PIDs html
getSequenceContext html
get_extreme_PIDs html
hclust_exposures html
logLikelihood html
lymphomaNature2013_mutCat_df 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-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:23: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:25: file link 'SomaticSignatures' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:11: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:18: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
normalize_df_per_dim html
plotExchangeSpectra html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/plotExchangeSpectra.Rd:38: file link 'theme_grey' in package 'ggplot2' does not exist and so has been treated as a topic
plotExchangeSpectra_indel html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/plotExchangeSpectra_indel.Rd:37: file link 'theme_grey' in package 'ggplot2' does not exist and so has been treated as a topic
plotExposuresConfidence html
plotExposuresConfidence_indel html
plot_SMC html
plot_exposures html
plot_strata html
read_entry html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/read_entry.Rd:50: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/read_entry.Rd:52: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
relateSigs html
repeat_df html
round_precision 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-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:42: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:53: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:54: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:64: 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-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:35: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:46: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:47: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:57: 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
sigs_pcawg 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
temp_trellis_rainfall_plot html
testSigs 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-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/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
trellis_rainfall_plot_old html
variateExp html
variateExpSingle 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_1.14.0.zip
* DONE (YAPSA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked