Charles Warden
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/COHCAP |
| Branch: RELEASE_3_10 |
| Last Commit: ba8bdbb |
| Last Changed Date: 2019-10-29 13:08:51 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:08:17 -0400 (Wed, 15 Apr 2020).
| Package 340/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| COHCAP 1.32.0 Charles Warden
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: COHCAP |
| Version: 1.32.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:COHCAP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings COHCAP_1.32.0.tar.gz |
| StartedAt: 2020-04-15 02:01:06 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:02:03 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 56.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COHCAP.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:COHCAP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings COHCAP_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/COHCAP.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COHCAP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COHCAP’ version ‘1.32.0’ * 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 ‘COHCAP’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE COHCAP.annotate: no visible binding for global variable ‘COHCAP.450k.UCSC’ COHCAP.annotate: no visible binding for global variable ‘COHCAP.450k.HMM’ COHCAP.annotate: no visible binding for global variable ‘COHCAP.27k’ COHCAP.integrate.avg.by.island: no visible binding for global variable ‘na.rm’ cor.test.est: no visible binding for global variable ‘na.rm’ cor.test.pvalue: no visible binding for global variable ‘na.rm’ Undefined global functions or variables: COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC na.rm * 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 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-3.10-bioc/meat/COHCAP.Rcheck/00check.log’ for details.
COHCAP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL COHCAP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘COHCAP’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Rcpp_BH_ttest.cpp -o Rcpp_BH_ttest.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o COHCAP.so RcppExports.o Rcpp_BH_ANOVA.o Rcpp_BH_ttest.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-COHCAP/00new/COHCAP/libs ** R ** 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 (COHCAP)
COHCAP.Rcheck/COHCAP-Ex.timings
| name | user | system | elapsed | |
| COHCAP.BSSeq.preprocess | 0.024 | 0.004 | 0.059 | |
| COHCAP.BSSeq_V2.methyl.table | 0.024 | 0.004 | 0.055 | |
| COHCAP.annotate | 1.924 | 0.084 | 2.042 | |
| COHCAP.avg.by.island | 3.712 | 0.256 | 4.096 | |
| COHCAP.avg.by.site | 3.588 | 0.228 | 3.892 | |
| COHCAP.denovo | 3.140 | 0.176 | 3.368 | |
| COHCAP.integrate.avg.by.island | 4.364 | 0.328 | 4.928 | |
| COHCAP.integrate.avg.by.site | 3.948 | 0.328 | 4.847 | |
| COHCAP.qc | 1.828 | 0.072 | 1.935 | |
| COHCAP.reformatFinalReport | 0.008 | 0.004 | 0.037 | |
| COHCAP.site | 2.924 | 0.164 | 3.247 | |