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This page was generated on 2023-10-20 09:38:10 -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 1645/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCASPAR 1.46.0  (landing page)
Douaa Mugahid , Lars Kaderali
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/RCASPAR
git_branch: RELEASE_3_17
git_last_commit: 195a62a
git_last_commit_date: 2023-04-25 10:19:57 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RCASPAR on kjohnson2


To the developers/maintainers of the RCASPAR 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: RCASPAR
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCASPAR_1.46.0.tar.gz
StartedAt: 2023-10-18 17:29:03 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 17:29:46 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 42.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RCASPAR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCASPAR_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RCASPAR.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 ‘RCASPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCASPAR’ version ‘1.46.0’
* 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 ‘RCASPAR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
kmplt_svrl: no visible global function definition for ‘lines’
kmplt_svrl: no visible global function definition for ‘legend’
logrnk: no visible global function definition for ‘pchisq’
pltprior: no visible global function definition for ‘persp’
weights_BLH: no visible global function definition for ‘optim’
Undefined global functions or variables:
  legend lines optim pchisq persp
Consider adding
  importFrom("graphics", "legend", "lines", "persp")
  importFrom("stats", "optim", "pchisq")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) STpredictor_BLH.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) STpredictor_BLH.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) STpredictor_BLH.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) STpredictor_BLH.Rd:79: Escaped LaTeX specials: \_ \_
checkRd: (-1) STpredictor_BLH.Rd:81: Escaped LaTeX specials: \_ \_
checkRd: (-1) STpredictor_BLH.Rd:82: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH.rd:45: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH.rd:46: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:17: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:40: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) logrnk.Rd:23: Escaped LaTeX specials: \_ \_
* 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
* 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-3.17-bioc-mac-arm64/meat/RCASPAR.Rcheck/00check.log’
for details.



Installation output

RCASPAR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RCASPAR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘RCASPAR’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCASPAR)

Tests output


Example timings

RCASPAR.Rcheck/RCASPAR-Ex.timings

nameusersystemelapsed
Bergamaschi0.0150.0040.027
RCASPAR-package0.3130.0370.543
STpredictor_BLH0.0380.0100.074
STpredictor_xvBLH0.3120.0340.528
deriv_weight_estimator_BLH0.0030.0020.007
deriv_weight_estimator_BLH_noprior0.0030.0020.006
kmplt0.0030.0010.006
kmplt_svrl0.0060.0010.012
logrnk0.0010.0000.004
pltgamma0.0020.0000.005
pltprior0.0020.0010.005
simpson0.0000.0010.001
survData0.0020.0010.004
survivAURC0.0980.0050.154
survivROC0.0230.0030.042
trapezoid000
weight_estimator_BLH000
weight_estimator_BLH_noprior0.0020.0020.009
weights_BLH0.0140.0030.028
weights_xvBLH0.0230.0040.041