Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:52 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the RJMCMCNucleosomes package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RJMCMCNucleosomes.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1616/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RJMCMCNucleosomes 1.18.0 (landing page) Astrid Deschênes
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: RJMCMCNucleosomes |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RJMCMCNucleosomes_1.18.0.tar.gz |
StartedAt: 2022-04-12 09:04:24 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 09:07:47 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 203.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RJMCMCNucleosomes.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RJMCMCNucleosomes_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/RJMCMCNucleosomes.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK * this is package ‘RJMCMCNucleosomes’ version ‘1.18.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘RJMCMCNucleosomes’ 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 * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 ‘/home/biocbuild/bbs-3.14-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log’ for details.
RJMCMCNucleosomes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL RJMCMCNucleosomes ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘RJMCMCNucleosomes’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c NucleoDirichlet.cpp -o NucleoDirichlet.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c Nucleosome.cpp -o Nucleosome.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c SegmentSeq.cpp -o SegmentSeq.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `gsl-config --cflags` -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o RJMCMCNucleosomes.so NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RJMCMCNucleosomes/00new/RJMCMCNucleosomes/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RJMCMCNucleosomes)
RJMCMCNucleosomes.Rcheck/tests/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > ## Run all tests presnt in the package > BiocGenerics:::testPackage("RJMCMCNucleosomes") Attaching package: 'BiocGenerics' 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, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname RJMCMCNucleosomes - Predicted nucleosomes Call: rjmcmc(reads = reads_demo_02, seqName = "chr_SYNTHETIC", nbrIterations = 1e+05, kMax = 30, lambda = 2, minInterval = 146, maxInterval = 490, minReads = 3, vSeed = 32) Number of nucleosomes: [1] 6 Nucleosomes positions: GRanges object with 6 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr_SYNTHETIC 10072 * [2] chr_SYNTHETIC 10241 * [3] chr_SYNTHETIC 10574 * [4] chr_SYNTHETIC 10656 * [5] chr_SYNTHETIC 10669 * [6] chr_SYNTHETIC 10744 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths [1] "Doing: out/results/rjmcmc_seg_1.rds" [1] "Done: out/results/rjmcmc_seg_1.rds" [1] "Doing: out/results/rjmcmc_seg_2.rds" [1] "Done: out/results/rjmcmc_seg_2.rds" [1] "Doing: out/results/rjmcmc_seg_3.rds" [1] "Done: out/results/rjmcmc_seg_3.rds" [1] "Doing: out/results/rjmcmc_seg_4.rds" [1] "Done: out/results/rjmcmc_seg_4.rds" [1] "Doing: out/results/rjmcmc_seg_5.rds" [1] "Done: out/results/rjmcmc_seg_5.rds" [1] "Doing: out/results/rjmcmc_seg_6.rds" [1] "Done: out/results/rjmcmc_seg_6.rds" [1] "Doing: out/results/rjmcmc_seg_7.rds" [1] "Done: out/results/rjmcmc_seg_7.rds" [1] "Doing: out/results/rjmcmc_seg_8.rds" [1] "Done: out/results/rjmcmc_seg_8.rds" [1] "Doing: out/results/rjmcmc_seg_9.rds" [1] "Done: out/results/rjmcmc_seg_9.rds" [1] "Doing: out/results/rjmcmc_seg_10.rds" [1] "Done: out/results/rjmcmc_seg_10.rds" [1] "Doing: out/results/rjmcmc_seg_11.rds" [1] "Done: out/results/rjmcmc_seg_11.rds" [1] "Doing: out/results/rjmcmc_seg_12.rds" [1] "Done: out/results/rjmcmc_seg_12.rds" [1] "Doing: out/results/rjmcmc_seg_13.rds" [1] "Done: out/results/rjmcmc_seg_13.rds" [1] "Doing: out/results/rjmcmc_seg_14.rds" [1] "Done: out/results/rjmcmc_seg_14.rds" [1] "Doing: out/results/rjmcmc_seg_15.rds" [1] "Done: out/results/rjmcmc_seg_15.rds" [1] "Doing: out/results/rjmcmc_seg_16.rds" [1] "Done: out/results/rjmcmc_seg_16.rds" [1] "Doing: out/results/rjmcmc_seg_17.rds" [1] "Done: out/results/rjmcmc_seg_17.rds" [1] "Doing: out/results/rjmcmc_seg_18.rds" [1] "Done: out/results/rjmcmc_seg_18.rds" [1] "Doing: out/results/rjmcmc_seg_19.rds" [1] "Done: out/results/rjmcmc_seg_19.rds" [1] "Doing: out/results/rjmcmc_seg_20.rds" [1] "Done: out/results/rjmcmc_seg_20.rds" [1] "Doing: out/results/rjmcmc_seg_21.rds" [1] "Done: out/results/rjmcmc_seg_21.rds" [1] "Doing: out/results/rjmcmc_seg_22.rds" [1] "Done: out/results/rjmcmc_seg_22.rds" [1] "Doing: out/results/rjmcmc_seg_23.rds" [1] "Done: out/results/rjmcmc_seg_23.rds" [1] "Doing: out/results/rjmcmc_seg_24.rds" [1] "Done: out/results/rjmcmc_seg_24.rds" [1] "Doing: out/results/rjmcmc_seg_25.rds" [1] "Done: out/results/rjmcmc_seg_25.rds" [1] "Doing: out/results/rjmcmc_seg_26.rds" [1] "Done: out/results/rjmcmc_seg_26.rds" [1] "Doing: out/results/rjmcmc_seg_27.rds" [1] "Done: out/results/rjmcmc_seg_27.rds" [1] "Doing: out/results/rjmcmc_seg_28.rds" [1] "Done: out/results/rjmcmc_seg_28.rds" [1] "Doing: out/results/rjmcmc_seg_29.rds" [1] "Done: out/results/rjmcmc_seg_29.rds" [1] "Doing: out/results/rjmcmc_seg_30.rds" [1] "Done: out/results/rjmcmc_seg_30.rds" [1] "Doing: out/results/rjmcmc_seg_31.rds" [1] "Done: out/results/rjmcmc_seg_31.rds" [1] "Doing: out/results/rjmcmc_seg_32.rds" [1] "Done: out/results/rjmcmc_seg_32.rds" [1] "Doing: out/results/rjmcmc_seg_33.rds" [1] "Done: out/results/rjmcmc_seg_33.rds" [1] "Doing: out/results/rjmcmc_seg_34.rds" [1] "Done: out/results/rjmcmc_seg_34.rds" [1] "Doing: out/results/rjmcmc_seg_35.rds" [1] "Done: out/results/rjmcmc_seg_35.rds" [1] "Doing: out/results/rjmcmc_seg_36.rds" [1] "Done: out/results/rjmcmc_seg_36.rds" [1] "Doing: out/results/rjmcmc_seg_37.rds" [1] "Done: out/results/rjmcmc_seg_37.rds" [1] "Doing: out/results/rjmcmc_seg_38.rds" [1] "Done: out/results/rjmcmc_seg_38.rds" [1] "Doing: out/results/rjmcmc_seg_39.rds" [1] "Done: out/results/rjmcmc_seg_39.rds" [1] "Doing: out/results/rjmcmc_seg_40.rds" [1] "Done: out/results/rjmcmc_seg_40.rds" [1] "Doing: out/results/rjmcmc_seg_41.rds" [1] "Done: out/results/rjmcmc_seg_41.rds" [1] "Doing: out/results/rjmcmc_seg_42.rds" [1] "Done: out/results/rjmcmc_seg_42.rds" [1] "Doing: out/results/rjmcmc_seg_43.rds" [1] "Done: out/results/rjmcmc_seg_43.rds" [1] "Doing: out/results/rjmcmc_seg_44.rds" [1] "Done: out/results/rjmcmc_seg_44.rds" [1] "Doing: out/results/rjmcmc_seg_45.rds" [1] "Done: out/results/rjmcmc_seg_45.rds" [1] "Doing: out/results/rjmcmc_seg_46.rds" [1] "Done: out/results/rjmcmc_seg_46.rds" [1] "Doing: out/results/rjmcmc_seg_47.rds" [1] "Done: out/results/rjmcmc_seg_47.rds" [1] "Doing: out/results/rjmcmc_seg_48.rds" [1] "Done: out/results/rjmcmc_seg_48.rds" [1] "Doing: out/results/rjmcmc_seg_49.rds" [1] "Done: out/results/rjmcmc_seg_49.rds" [1] "Doing: out/results/rjmcmc_seg_50.rds" [1] "Done: out/results/rjmcmc_seg_50.rds" [1] "Doing: out/results/rjmcmc_seg_51.rds" [1] "Done: out/results/rjmcmc_seg_51.rds" [1] "Doing: out/results/rjmcmc_seg_52.rds" [1] "Done: out/results/rjmcmc_seg_52.rds" [1] "Doing: out/results/rjmcmc_seg_53.rds" [1] "Done: out/results/rjmcmc_seg_53.rds" [1] "Doing: out/results/rjmcmc_seg_54.rds" [1] "Done: out/results/rjmcmc_seg_54.rds" [1] "Doing: out/results/rjmcmc_seg_55.rds" [1] "Done: out/results/rjmcmc_seg_55.rds" [1] "Doing: out/results/rjmcmc_seg_56.rds" [1] "Done: out/results/rjmcmc_seg_56.rds" RJMCMCNucleosomes - Predicted nucleosomes Before and After Post-Treatment BEFORE POST-TREATMENT Number of nucleosomes: [1] 102 Nucleosomes positions: GRanges object with 102 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr_SYNTHETIC 1255 * [2] chr_SYNTHETIC 2259 * [3] chr_SYNTHETIC 3623 * [4] chr_SYNTHETIC 4259 * [5] chr_SYNTHETIC 5348 * ... ... ... ... [98] chr_SYNTHETIC 53427 * [99] chr_SYNTHETIC 54220 * [100] chr_SYNTHETIC 54771 * [101] chr_SYNTHETIC 55358 * [102] chr_SYNTHETIC 55936 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths AFTER POST-TREATMENT Number of nucleosomes: [1] 89 Nucleosomes positions: GRanges object with 89 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr_SYNTHETIC 1255 * [2] chr_SYNTHETIC 2259 * [3] chr_SYNTHETIC 3623 * [4] chr_SYNTHETIC 4259 * [5] chr_SYNTHETIC 5348 * ... ... ... ... [85] chr_SYNTHETIC 53286 * [86] chr_SYNTHETIC 54220 * [87] chr_SYNTHETIC 54771 * [88] chr_SYNTHETIC 55358 * [89] chr_SYNTHETIC 55936 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths RJMCMCNucleosomes - Predicted nucleosomes Number of nucleosomes: [1] 11 Nucleosomes positions: GRanges object with 11 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr_SYNTHETIC 10077 * [2] chr_SYNTHETIC 10236 * [3] chr_SYNTHETIC 10406 * [4] chr_SYNTHETIC 10571 * [5] chr_SYNTHETIC 10744 * [6] chr_SYNTHETIC 10842 * [7] chr_SYNTHETIC 10846 * [8] chr_SYNTHETIC 10896 * [9] chr_SYNTHETIC 10906 * [10] chr_SYNTHETIC 11410 * [11] chr_SYNTHETIC 11580 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths [1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds" [1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds" [1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds" [1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds" [1] "Doing: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds" [1] "Done: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds" RUNIT TEST PROTOCOL -- Tue Apr 12 09:07:44 2022 *********************************************** Number of test functions: 86 Number of errors: 0 Number of failures: 0 1 Test Suite : RJMCMCNucleosomes RUnit Tests - 86 test functions, 0 errors, 0 failures Number of test functions: 86 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 19.677 1.291 37.692
RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes-Ex.timings
name | user | system | elapsed | |
RJMCMC_result | 0.53 | 0.10 | 0.63 | |
mergeAllRDSFiles | 0.120 | 0.000 | 0.119 | |
mergeAllRDSFilesFromDirectory | 0.106 | 0.004 | 0.110 | |
mergeRDSFiles | 0.107 | 0.000 | 0.108 | |
plotNucleosomes | 0.246 | 0.004 | 0.250 | |
postMerge | 0.310 | 0.036 | 0.346 | |
postTreatment | 0.319 | 0.028 | 0.347 | |
print.rjmcmcNucleosomes | 0.011 | 0.000 | 0.010 | |
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment | 0.079 | 0.008 | 0.086 | |
print.rjmcmcNucleosomesMerge | 0.12 | 0.00 | 0.12 | |
reads_demo_01 | 0.035 | 0.004 | 0.038 | |
reads_demo_02 | 0.043 | 0.000 | 0.043 | |
rjmcmc | 0.074 | 0.000 | 0.074 | |
rjmcmcCHR | 0.057 | 0.004 | 0.061 | |
rjmcmcNucleo | 0.046 | 0.000 | 0.047 | |
runCHR | 0.075 | 0.004 | 0.080 | |
segmentation | 0.127 | 0.000 | 0.127 | |
validateDirectoryParameters | 0.001 | 0.000 | 0.000 | |
validatePlotNucleosomesParameters | 0.003 | 0.000 | 0.003 | |
validatePrepMergeParameters | 0.002 | 0.000 | 0.003 | |
validateRDSFilesParameters | 0.000 | 0.000 | 0.001 | |
validateRJMCMCParameters | 0.016 | 0.000 | 0.017 | |
validateSegmentationParameters | 0.021 | 0.000 | 0.021 | |