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CHECK report for multiscan on merida1

This page was generated on 2019-04-16 11:54:52 -0400 (Tue, 16 Apr 2019).

Package 1026/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiscan 1.42.0
Mizanur Khondoker
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/multiscan
Branch: RELEASE_3_8
Last Commit: 9a68631
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: multiscan
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:multiscan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings multiscan_1.42.0.tar.gz
StartedAt: 2019-04-16 01:30:53 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:31:28 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 35.0 seconds
RetCode: 0
Status:  OK 
CheckDir: multiscan.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:multiscan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings multiscan_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/multiscan.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiscan/DESCRIPTION’ ... OK
* this is package ‘multiscan’ version ‘1.42.0’
* 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 ‘multiscan’ 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
File ‘multiscan/R/zzz.R’:
  .onAttach calls:
    cat(paste("*** Loaded multiscan Version", packageDescription("multiscan")$Version),     "*** \n")
    cat("Type 'vignette(\"multiscan\")' to view the package vignette.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

multiscan: no visible global function definition for ‘na.omit’
multiscan: no visible global function definition for ‘na.fail’
multiscan: no visible binding for global variable ‘median’
plot.multiscan: no visible global function definition for ‘par’
plot.multiscan: no visible global function definition for ‘plot’
plot.multiscan: no visible global function definition for ‘points’
plot.multiscan: no visible global function definition for ‘lines’
plot.multiscan: no visible global function definition for ‘legend’
plot.multiscan: no visible global function definition for
  ‘dev.interactive’
plot.multiscan: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline dev.interactive legend lines median na.fail na.omit par plot
  points
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "points")
  importFrom("stats", "median", "na.fail", "na.omit")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/multiscan.Rcheck/00check.log’
for details.



Installation output

multiscan.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL multiscan
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘multiscan’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c multiscan.c -o multiscan.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o multiscan.so multiscan.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/multiscan/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** Loaded multiscan Version 1.42.0 *** 
Type 'vignette("multiscan")' to view the package vignette.
* DONE (multiscan)

Tests output


Example timings

multiscan.Rcheck/multiscan-Ex.timings

nameusersystemelapsed
multiscan2.9480.0243.058
plot.multiscan1.4200.0171.449