Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:28:37 -0400 (Thu, 12 Apr 2018).
Package 1467/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
YAPSA 1.4.0 Daniel Huebschmann
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK |
Package: YAPSA |
Version: 1.4.0 |
Command: rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_1.4.0.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_1.4.0.tar.gz |
StartedAt: 2018-04-12 03:52:58 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 04:01:21 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 502.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: YAPSA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf YAPSA.buildbin-libdir YAPSA.Rcheck && mkdir YAPSA.buildbin-libdir YAPSA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=YAPSA.buildbin-libdir YAPSA_1.4.0.tar.gz >YAPSA.Rcheck\00install.out 2>&1 && cp YAPSA.Rcheck\00install.out YAPSA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=YAPSA.buildbin-libdir --install="check:YAPSA-install.out" --force-multiarch --no-vignettes --timings YAPSA_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/YAPSA.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'YAPSA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'YAPSA' version '1.4.0' * 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 'YAPSA' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:49: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:51: missing file link 'motifMatrix' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:18: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:22: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:86: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:88: missing file link 'motifMatrix' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:39: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:43: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:20: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:22: missing file link 'SomaticSignatures' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:10: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:15: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:40: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:51: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:52: missing file link 'kmerFrequency' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:62: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:29: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:40: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:41: missing file link 'kmerFrequency' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:51: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/translate_to_hg19.Rd:31: missing file link 'BSgenome.Hsapiens.UCSC.hg19' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/YAPSA.Rcheck/00install.out' for details. * 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 ** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed run_SMC 6.16 0.19 6.35 * 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 WARNING See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/YAPSA.Rcheck/00check.log' for details.
YAPSA.Rcheck/00install.out
install for i386 * installing *source* package 'YAPSA' ... ** R ** data ** inst ** preparing 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-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:49: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:51: missing file link 'motifMatrix' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:18: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:22: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:86: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_VR.Rd:88: missing file link 'motifMatrix' create_mutation_catalogue_from_df html finding level-2 HTML links ... done Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:39: missing file link 'mutationContext' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/create_mutation_catalogue_from_df.Rd:43: missing file link 'mutationContext' 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-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:20: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:22: missing file link 'SomaticSignatures' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:10: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/normalizeMotifs_otherRownames.Rd:15: missing file link 'normalizeMotifs' 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-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:40: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:51: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:52: missing file link 'kmerFrequency' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_correction.Rd:62: missing file link 'normalizeMotifs' run_kmer_frequency_normalization html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:29: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:40: missing file link 'normalizeMotifs' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:41: missing file link 'kmerFrequency' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/run_kmer_frequency_normalization.Rd:51: missing file link 'normalizeMotifs' 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-3.6-bioc/tmpdir/Rtmpgv3JD5/R.INSTALL3ad07bf03ea5/YAPSA/man/translate_to_hg19.Rd:31: missing file link 'BSgenome.Hsapiens.UCSC.hg19' 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_1.4.0.zip * DONE (YAPSA) In R CMD INSTALL In R CMD INSTALL
YAPSA.Rcheck/tests_i386/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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(YAPSA) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: ggplot2 Loading required package: grid > > test_check("YAPSA") YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand information missing, set to "+". YAPSA:::makeVRangesFromDataFrame::in_PID.field found. Retrieving PID information. YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found. Retrieving subgroup information. == testthat results =========================================================== OK: 63 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 13.45 0.56 14.12 |
YAPSA.Rcheck/tests_x64/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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(YAPSA) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: ggplot2 Loading required package: grid > > test_check("YAPSA") YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand information missing, set to "+". YAPSA:::makeVRangesFromDataFrame::in_PID.field found. Retrieving PID information. YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found. Retrieving subgroup information. == testthat results =========================================================== OK: 63 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 14.78 0.53 15.40 |
YAPSA.Rcheck/examples_i386/YAPSA-Ex.timings
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YAPSA.Rcheck/examples_x64/YAPSA-Ex.timings
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