Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 394/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CODEX 1.32.0  (landing page)
Yuchao Jiang
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CODEX
git_branch: RELEASE_3_17
git_last_commit: 8392623
git_last_commit_date: 2023-04-25 10:37:02 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for CODEX on kjohnson2


To the developers/maintainers of the CODEX package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CODEX
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CODEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CODEX_1.32.0.tar.gz
StartedAt: 2023-10-17 10:56:09 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 11:03:30 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 441.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CODEX.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CODEX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CODEX_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CODEX.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CODEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CODEX’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Rsamtools', 'GenomeInfoDb', 'BSgenome.Hsapiens.UCSC.hg19',
  'IRanges', 'Biostrings', 'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘CODEX’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
choiceofK: no visible global function definition for ‘pdf’
choiceofK: no visible global function definition for ‘par’
choiceofK: no visible global function definition for ‘dev.off’
getbambed: no visible global function definition for ‘read.table’
normalize : <anonymous>: no visible global function definition for
  ‘smooth.spline’
normalize : <anonymous>: no visible global function definition for
  ‘predict’
normalize: no visible global function definition for ‘glm’
normalize: no visible binding for global variable ‘poisson’
normalize: no visible global function definition for ‘lm’
normalize2 : <anonymous>: no visible global function definition for
  ‘smooth.spline’
normalize2 : <anonymous>: no visible global function definition for
  ‘predict’
normalize2: no visible global function definition for ‘glm’
normalize2: no visible binding for global variable ‘poisson’
normalize2: no visible global function definition for ‘lm’
Undefined global functions or variables:
  dev.off glm lm par pdf poisson predict read.table smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "glm", "lm", "poisson", "predict", "smooth.spline")
  importFrom("utils", "read.table")
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
normalize   24.171  0.624  41.074
normalize2  19.282  0.380  34.214
getcoverage  8.592  0.433  13.249
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CODEX.Rcheck/00check.log’
for details.



Installation output

CODEX.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CODEX
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘CODEX’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CODEX)

Tests output


Example timings

CODEX.Rcheck/CODEX-Ex.timings

nameusersystemelapsed
bambedObjDemo0.0010.0010.003
choiceofK0.0490.0050.084
coverageObjDemo000
gcDemo0.0010.0000.005
getbambed0.0290.0050.050
getcoverage 8.592 0.43313.249
getgc0.4390.0410.726
getmapp0.6730.0081.041
mappDemo000
mapp_ref0.0150.0000.024
mappability0.0010.0000.002
normObjDemo0.0000.0010.000
normalize24.171 0.62441.074
normalize219.282 0.38034.214
qc0.0230.0010.038
qcObjDemo000
segment0.7820.0331.275