Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 58/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
altcdfenvs 2.67.0  (landing page)
Laurent Gautier
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/altcdfenvs
git_branch: devel
git_last_commit: f8437dc
git_last_commit_date: 2024-04-30 10:12:20 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for altcdfenvs on merida1

To the developers/maintainers of the altcdfenvs package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/altcdfenvs.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: altcdfenvs
Version: 2.67.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:altcdfenvs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings altcdfenvs_2.67.0.tar.gz
StartedAt: 2024-06-09 23:41:29 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 23:45:17 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 228.0 seconds
RetCode: 0
Status:   OK  
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:altcdfenvs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings altcdfenvs_2.67.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/altcdfenvs.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.67.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'Biobase', 'affy', 'makecdfenv',
  'Biostrings', 'hypergraph'
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 ‘altcdfenvs’ 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 code 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘Biostrings’ ‘hypergraph’ ‘makecdfenv’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildCdfEnv.biostrings: no visible global function definition for
  ‘validObject’
buildCdfEnv.biostrings: no visible global function definition for ‘is’
buildCdfEnv.biostrings: no visible global function definition for ‘new’
buildCdfEnv.biostrings: no visible global function definition for
  ‘update’
buildCdfEnv.biostrings: no visible global function definition for
  ‘xy2indices’
buildCdfEnv.matchprobes: no visible global function definition for ‘is’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘new’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘update’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘xy2indices’
copyCdfEnvAffy: no visible global function definition for ‘copyEnv’
countduplicated: no visible global function definition for ‘is’
countduplicated: no visible global function definition for ‘as’
geneNames.CdfEnvAffy: no visible global function definition for ‘as’
getCdfEnvAffy: no visible global function definition for ‘is’
getCdfEnvAffy: no visible global function definition for ‘getCdfInfo’
index2xy.CdfEnvAffy: no visible global function definition for
  ‘indices2xy’
indexProbes.CdfEnvAffy: no visible global function definition for ‘as’
matchAffyProbes: no visible global function definition for
  ‘DNAStringSet’
matchAffyProbes: no visible global function definition for ‘DNAString’
matchAffyProbes: no visible global function definition for ‘PDict’
matchAffyProbes: no visible global function definition for ‘matchPDict’
matchAffyProbes: no visible global function definition for ‘new’
removeIndex: no visible global function definition for ‘as’
unique.CdfEnvAffy: no visible global function definition for ‘as’
validAffyBatch: no visible global function definition for ‘is’
validCdfEnvAffy: no visible global function definition for ‘as’
wrapCdfEnvAffy: no visible global function definition for ‘new’
xy2index.CdfEnvAffy: no visible global function definition for
  ‘xy2indices’
[,CdfEnvAffy-character-missing-missing: no visible global function
  definition for ‘as’
coerce,CdfEnvAffy-Cdf: no visible global function definition for ‘new’
combine,AffyProbesMatch-AffyProbesMatch: no visible global function
  definition for ‘new’
geneNames,CdfEnvAffy: no visible global function definition for ‘as’
indexProbes,CdfEnvAffy-character: no visible global function definition
  for ‘as’
show,CdfEnvAffy: no visible global function definition for ‘as’
toHypergraph,AffyProbesMatch : <anonymous>: no visible global function
  definition for ‘Hyperedge’
toHypergraph,AffyProbesMatch: no visible global function definition for
  ‘new’
toHypergraph,CdfEnvAffy : <anonymous>: no visible global function
  definition for ‘Hyperedge’
toHypergraph,CdfEnvAffy: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  DNAString DNAStringSet Hyperedge PDict as copyEnv getCdfInfo
  indices2xy is matchPDict new update validObject xy2indices
Consider adding
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "update")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
removeIndex      15.307  0.164  18.261
CdfEnvAffy-class  7.301  0.227   8.570
matchAffyProbes   7.064  0.353   8.207
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/altcdfenvs.Rcheck/00check.log’
for details.


Installation output

altcdfenvs.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘altcdfenvs’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for ‘toHypergraph’ with signature ‘"CdfEnvAffy"’: no definition for class “CdfEnvAffy”
** 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 (altcdfenvs)

Tests output


Example timings

altcdfenvs.Rcheck/altcdfenvs-Ex.timings

nameusersystemelapsed
AffyProbesMatch-class0.0020.0010.003
CdfEnvAffy-class7.3010.2278.570
appendCdfEnvAffy0.0070.0060.013
cdfenv0.0010.0000.001
cdfenvEx0.0030.0050.009
getxy.probeseq0.0000.0010.000
index2xy0.0000.0010.000
matchAffyProbes7.0640.3538.207
plot.CdfEnvAffy0.0000.0000.001
removeIndex15.307 0.16418.261
unique.CdfEnvAffy000
utils.FASTA0.0080.0020.014
validAffyBatch0.0000.0010.001