Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:51 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 megadepth package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/megadepth.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 1079/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
megadepth 1.4.0 (landing page) David Zhang
| 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: megadepth |
Version: 1.4.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:megadepth.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings megadepth_1.4.0.tar.gz |
StartedAt: 2022-04-12 22:24:25 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 22:27:20 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 175.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: megadepth.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:megadepth.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings megadepth_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/megadepth.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'megadepth/DESCRIPTION' ... OK * this is package 'megadepth' version '1.4.0' * 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 whether package 'megadepth' 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 * 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 * 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 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_coverage 5.88 0.53 6.73 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_coverage 6.76 0.21 7.28 * 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: OK
megadepth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/megadepth_1.4.0.tar.gz && rm -rf megadepth.buildbin-libdir && mkdir megadepth.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=megadepth.buildbin-libdir megadepth_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL megadepth_1.4.0.zip && rm megadepth_1.4.0.tar.gz megadepth_1.4.0.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 158k 100 158k 0 0 312k 0 --:--:-- --:--:-- --:--:-- 312k 100 158k 100 158k 0 0 312k 0 --:--:-- --:--:-- --:--:-- 312k install for i386 * installing *source* package 'megadepth' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'megadepth' finding HTML links ... done bam_to_bigwig html bam_to_junctions html get_coverage html install_megadepth html megadepth_cmd html process_junction_table html read_coverage html read_junction_table 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 'megadepth' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'megadepth' as megadepth_1.4.0.zip * DONE (megadepth) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'megadepth' successfully unpacked and MD5 sums checked
megadepth.Rcheck/tests_i386/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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(megadepth) > > ## Install the latest version if necessary > install_megadepth(force = TRUE) The latest megadepth version is 1.2.0 This is not an interactive session, therefore megadepth has been installed temporarily to C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgDs1KR/megadepth.exe > > test_check("megadepth") Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam" Read 3 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam" Read 3 records # of overlapping pairs: 0 building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw The latest megadepth version is 1.2.0 Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgDs1KR/test.bam.all.bw Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test3.bam" WARNING: writing BigWigs (--bigwig) is not supported on Windows at this time, no BigWig file(s) will be written, but any other options will still be processed. Read 12 records # of overlapping pairs: 3 building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing http://stingray.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpgDs1KR/test.bam.all.bw Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ] > > proc.time() user system elapsed 7.50 0.96 15.98 |
megadepth.Rcheck/tests_x64/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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(megadepth) > > ## Install the latest version if necessary > install_megadepth(force = TRUE) The latest megadepth version is 1.2.0 This is not an interactive session, therefore megadepth has been installed temporarily to C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpYFJRVW/megadepth.exe > > test_check("megadepth") Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam" Read 3 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/long_reads.bam" Read 3 records # of overlapping pairs: 0 building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test.bam.all.bw The latest megadepth version is 1.2.0 Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpYFJRVW/test.bam.all.bw Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test3.bam" WARNING: writing BigWigs (--bigwig) is not supported on Windows at this time, no BigWig file(s) will be written, but any other options will still be processed. Read 12 records # of overlapping pairs: 3 building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing http://stingray.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed unsorted interval: chr10 4359156 4359188 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. total number of annotations in collapsed: 1 Processing C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpYFJRVW/test.bam.all.bw Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 Processing BAM: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/megadepth/tests/test2.bam" Read 7 records # of overlapping pairs: 0 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ] > > proc.time() user system elapsed 6.59 0.79 13.46 |
megadepth.Rcheck/examples_i386/megadepth-Ex.timings
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megadepth.Rcheck/examples_x64/megadepth-Ex.timings
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