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This page was generated on 2024-02-22 11:36:11 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1513/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaMethods 1.94.0  (landing page)
Henning Redestig
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/pcaMethods
git_branch: RELEASE_3_18
git_last_commit: 5bb47fc
git_last_commit_date: 2023-10-24 09:37:22 -0500 (Tue, 24 Oct 2023)
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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for pcaMethods on nebbiolo2


To the developers/maintainers of the pcaMethods package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pcaMethods.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: pcaMethods
Version: 1.94.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:pcaMethods.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings pcaMethods_1.94.0.tar.gz
StartedAt: 2024-02-22 01:07:52 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 01:13:09 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 317.6 seconds
RetCode: 0
Status:   OK  
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:pcaMethods.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings pcaMethods_1.94.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/pcaMethods.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.94.0’
* package encoding: UTF-8
* 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 ‘pcaMethods’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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
BPCA_initmodel: no visible global function definition for ‘cov’
Q2: no visible global function definition for ‘txtProgressBar’
Q2: no visible global function definition for ‘setTxtProgressBar’
Q2: no visible global function definition for ‘cor’
RnipalsPca: no visible global function definition for ‘na.omit’
cvseg : <anonymous>: no visible global function definition for
  ‘na.omit’
llsImpute: no visible global function definition for ‘cor’
nlpca: no visible global function definition for ‘runif’
nlpca: no visible global function definition for ‘rnorm’
plot.pcaRes: no visible global function definition for ‘gray’
plot.pcaRes: no visible global function definition for ‘barplot’
plot.pcaRes: no visible global function definition for ‘legend’
plotPcs : panel: no visible global function definition for ‘abline’
plotPcs : panel: no visible global function definition for ‘lines’
plotPcs : panel: no visible global function definition for ‘points’
plotPcs : panel: no visible global function definition for ‘text’
plotPcs: no visible global function definition for ‘pairs’
ppca: no visible global function definition for ‘rnorm’
ppca: no visible global function definition for ‘cov’
robustSvd: no visible binding for global variable ‘median’
simpleEllipse: no visible global function definition for ‘qf’
svdImpute: no visible global function definition for ‘prcomp’
svdPca: no visible global function definition for ‘prcomp’
plot,pcaRes: no visible global function definition for ‘gray’
plot,pcaRes: no visible global function definition for ‘barplot’
plot,pcaRes: no visible global function definition for ‘legend’
slplot,pcaRes: no visible global function definition for ‘par’
slplot,pcaRes: no visible global function definition for ‘layout’
slplot,pcaRes: no visible global function definition for ‘abline’
slplot,pcaRes: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline barplot cor cov gray layout legend lines median na.omit pairs
  par points prcomp qf rnorm runif setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "barplot", "layout", "legend",
             "lines", "pairs", "par", "points", "text")
  importFrom("stats", "cor", "cov", "median", "na.omit", "prcomp", "qf",
             "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
kEstimate 64.840  0.347  71.757
robustSvd  7.989  0.004   7.993
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘missingValues.Rnw’ using ‘UTF-8’... OK
  ‘outliers.Rnw’ using ‘UTF-8’... OK
  ‘pcaMethods.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.



Installation output

pcaMethods.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL pcaMethods
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘pcaMethods’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c nipals.cpp -o nipals.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o pcaMethods.so RcppExports.o nipals.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-pcaMethods/00new/pcaMethods/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘loadings’ in package ‘pcaMethods’
** 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 (pcaMethods)

Tests output


Example timings

pcaMethods.Rcheck/pcaMethods-Ex.timings

nameusersystemelapsed
DModX-pcaRes-method0.0730.0050.077
Q20.260.000.26
R2VX-pcaRes-method0.0270.0000.027
RnipalsPca0.3870.0000.388
biplot-methods0.0160.0000.015
bpca1.1110.0201.131
cvseg0.0180.0020.020
fitted-methods0.0130.0010.013
kEstimate64.840 0.34771.757
kEstimateFast0.3660.0000.366
leverage-pcaRes-method0.0120.0000.012
llsImpute0.1730.0400.214
nipalsPca0.0090.0000.009
nlpca1.4690.0081.478
nni0.1140.0040.118
pca1.0120.0041.017
plot.pcaRes0.1870.0080.195
plotPcs0.0290.0040.033
ppca0.1300.0040.134
predict-methods0.0090.0000.009
prep0.0010.0000.001
rediduals-methods0.0080.0000.008
robustPca3.630.003.63
robustSvd7.9890.0047.993
slplot-pcaRes-method0.0180.0000.018
svdImpute0.0730.0000.073
svdPca0.0110.0000.012
wasna-pcaRes-method0.0190.0040.023