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CHECK report for COHCAP on malbec2

This page was generated on 2020-10-17 11:54:36 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE COHCAP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 350/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.34.1
Charles Warden
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/COHCAP
Branch: RELEASE_3_11
Last Commit: 5882753
Last Changed Date: 2020-04-30 15:46:49 -0400 (Thu, 30 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: COHCAP
Version: 1.34.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:COHCAP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings COHCAP_1.34.1.tar.gz
StartedAt: 2020-10-17 00:07:28 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:08:14 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 45.7 seconds
RetCode: 0
Status:  OK 
CheckDir: COHCAP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:COHCAP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings COHCAP_1.34.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/COHCAP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.34.1’
* 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-3.11-bioc/meat/COHCAP.Rcheck/00check.log’
for details.



Installation output

COHCAP.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL COHCAP
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘COHCAP’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Rcpp_BH_linear_regression.cpp -o Rcpp_BH_linear_regression.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/lib -L/usr/local/lib -o COHCAP.so RcppExports.o Rcpp_BH_ANOVA.o Rcpp_BH_linear_regression.o Rcpp_BH_ttest.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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)

Tests output


Example timings

COHCAP.Rcheck/COHCAP-Ex.timings

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.0150.0140.153
COHCAP.BSSeq_V2.methyl.table0.0310.0000.031
COHCAP.annotate1.5700.0321.711
COHCAP.avg.by.island1.8530.0551.938
COHCAP.avg.by.site2.2850.0972.381
COHCAP.denovo1.6300.0701.702
COHCAP.integrate.avg.by.island1.6290.0811.719
COHCAP.integrate.avg.by.site1.5680.0791.647
COHCAP.qc1.0580.0491.110
COHCAP.reformatFinalReport0.0070.0000.007
COHCAP.site1.6400.0661.705