Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the HMMcopy package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HMMcopy.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 871/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HMMcopy 1.34.0 (landing page) Daniel Lai
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: HMMcopy |
Version: 1.34.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HMMcopy.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HMMcopy_1.34.0.tar.gz |
StartedAt: 2021-10-14 10:11:28 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:11:54 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 26.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HMMcopy.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HMMcopy.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HMMcopy_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/HMMcopy.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HMMcopy/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HMMcopy’ version ‘1.34.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘HMMcopy’ 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 ... WARNING Missing link or links in documentation object 'HMMcopy-dataset.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'HMMcopy-input.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'HMMcopy-output.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'correctReadcount.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link or links in documentation object 'wigsToRangedData.Rd': ‘[IRanges:RangedData-class]{RangedData}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 compiled code ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/HMMcopy.Rcheck/00check.log’ for details.
HMMcopy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL HMMcopy ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘HMMcopy’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c forward_backward.c -o forward_backward.o forward_backward.c: In function ‘forward_backward’: forward_backward.c:28:13: warning: unused variable ‘tmp’ [-Wunused-variable] 28 | int K, T, tmp; | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c register.c -o register.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c viterbi.c -o viterbi.o viterbi.c: In function ‘viterbi’: viterbi.c:21:13: warning: unused variable ‘tmp’ [-Wunused-variable] 21 | int K, T, tmp; | ^~~ gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o HMMcopy.so forward_backward.o register.o viterbi.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-HMMcopy/00new/HMMcopy/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 (HMMcopy)
HMMcopy.Rcheck/HMMcopy-Ex.timings
name | user | system | elapsed | |
HMMcopy-input | 0.025 | 0.000 | 0.026 | |
HMMcopy-output | 0.116 | 0.065 | 0.181 | |
HMMcopy-package | 4.366 | 0.091 | 4.447 | |
HMMcopy-visualize | 1.695 | 0.016 | 1.699 | |
HMMsegment | 0.131 | 0.000 | 0.131 | |
correctReadcount | 0.090 | 0.012 | 0.102 | |
wigsToRangedData | 0.038 | 0.000 | 0.038 | |