Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:15 -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 DegNorm package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DegNorm.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 473/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DegNorm 1.4.0 (landing page) Ji-Ping Wang
| 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: DegNorm |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DegNorm.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DegNorm_1.4.0.tar.gz |
StartedAt: 2022-04-12 07:05:39 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 07:11:12 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 332.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DegNorm.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DegNorm.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DegNorm_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/DegNorm.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 ‘DegNorm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DegNorm’ 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 for sufficient/correct file permissions ... OK * checking whether package ‘DegNorm’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.5Mb sub-directories of 1Mb or more: doc 4.7Mb extdata 2.1Mb libs 3.9Mb * 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 ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed read_coverage_batch 5.083 0.277 82.427 degnorm 1.595 0.148 47.024 * 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/DegNorm.Rcheck/00check.log’ for details.
DegNorm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DegNorm ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘DegNorm’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c degnormCPP.cpp -o degnormCPP.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o DegNorm.so RcppExports.o degnormCPP.o -fopenmp -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-DegNorm/00new/DegNorm/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 (DegNorm)
DegNorm.Rcheck/DegNorm-Ex.timings
name | user | system | elapsed | |
PlotFunctions | 0.786 | 0.052 | 0.838 | |
coverage_res_chr21 | 0.276 | 0.012 | 0.288 | |
degnorm | 1.595 | 0.148 | 47.024 | |
plot_coverage | 0.516 | 0.012 | 0.529 | |
read_coverage_batch | 5.083 | 0.277 | 82.427 | |
res_DegNorm_chr21 | 0.037 | 0.012 | 0.049 | |
summary_CoverageClass | 0.090 | 0.004 | 0.094 | |
summary_DegNormClass | 0.040 | 0.008 | 0.048 | |