Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:27:25 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the DSS package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 513/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DSS 2.38.0 (landing page) Hao Wu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: DSS |
Version: 2.38.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DSS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DSS_2.38.0.tar.gz |
StartedAt: 2021-05-06 01:08:22 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:13:05 -0400 (Thu, 06 May 2021) |
EllapsedTime: 282.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DSS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DSS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DSS_2.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/DSS.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DSS/DESCRIPTION’ ... OK * this is package ‘DSS’ version ‘2.38.0’ * 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 ‘DSS’ 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 ... NOTE Namespace in Imports field not imported from: ‘DelayedArray’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE est.phi.naive: no visible global function definition for ‘rowVars’ est.prior.BSseq.logN: no visible global function definition for ‘rowVars’ Undefined global functions or variables: rowVars * 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 compiled code ... NOTE Note: information on .o files is not available * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.12-bioc/meat/DSS.Rcheck/00check.log’ for details.
DSS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL DSS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘DSS’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c compute_var_smooth.c -o compute_var_smooth.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c filter.c -o filter.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nitem.c -o nitem.o gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o DSS.so compute_var_smooth.o filter.o nitem.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-DSS/00new/DSS/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 (DSS)
DSS.Rcheck/DSS-Ex.timings
name | user | system | elapsed | |
DMLfit.multiFactor | 0 | 0 | 0 | |
DMLtest | 0.004 | 0.000 | 0.000 | |
DMLtest.multiFactor | 0.004 | 0.000 | 0.000 | |
DSS.DE | 0.376 | 0.024 | 0.401 | |
RRBS | 0.044 | 0.000 | 0.043 | |
SeqCountSet-class | 0.376 | 0.000 | 0.376 | |
callDML | 0 | 0 | 0 | |
callDMR | 0 | 0 | 0 | |
design | 0.028 | 0.004 | 0.033 | |
dispersion | 0.164 | 0.000 | 0.164 | |
estDispersion | 0.404 | 0.032 | 0.436 | |
estNormFactors | 0.008 | 0.004 | 0.012 | |
makeBSseqData | 2.032 | 0.024 | 2.476 | |
normalizationFactor | 0.008 | 0.000 | 0.007 | |
seqData | 0.004 | 0.000 | 0.005 | |
showOneDMR | 0 | 0 | 0 | |
waldTest | 0.196 | 0.004 | 0.200 | |