Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:04:26 -0400 (Mon, 18 Oct 2021).

CHECK results for BAC on merida1

To the developers/maintainers of the BAC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BAC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 104/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BAC 1.53.0  (landing page)
Raphael Gottardo
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/BAC
git_branch: master
git_last_commit: c132ac8
git_last_commit_date: 2021-05-19 11:40:12 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BAC
Version: 1.53.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BAC_1.53.0.tar.gz
StartedAt: 2021-10-18 01:01:00 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 01:02:42 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 102.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BAC.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BAC_1.53.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BAC.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BAC’ version ‘1.53.0’
* 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 ‘BAC’ 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
BAC: no visible global function definition for ‘median’
BAC: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median
Consider adding
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: BAC.Rd:37-38: Dropping empty section \note
prepare_Rd: CallRegions.Rd:21-23: Dropping empty section \details
prepare_Rd: CallRegions.Rd:34-35: Dropping empty section \note
* 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
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BAC/libs/BAC.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
CallRegions 34.279  0.069  34.390
BAC         32.926  0.088  33.062
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BAC.Rcheck/00check.log’
for details.



Installation output

BAC.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BAC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BAC’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BAC.c -o BAC.o
BAC.c:65:15: warning: implicit conversion from 'double' to 'int' changes value from 0.01 to 0 [-Wliteral-conversion]
        w=dvector(*G,0.01);
          ~~~~~~~    ^~~~
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c util.c -o util.o
clang -mmacosx-version-min=10.13 -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 BAC.so BAC.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-BAC/00new/BAC/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 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 (BAC)

Tests output


Example timings

BAC.Rcheck/BAC-Ex.timings

nameusersystemelapsed
BAC32.926 0.08833.062
CallRegions34.279 0.06934.390