Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1680/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCASPAR 1.52.0  (landing page)
Douaa Mugahid , Lars Kaderali
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RCASPAR
git_branch: RELEASE_3_20
git_last_commit: 4df789d
git_last_commit_date: 2024-10-29 09:37:14 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 RCASPAR on nebbiolo2

To the developers/maintainers of the RCASPAR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCASPAR.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: RCASPAR
Version: 1.52.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RCASPAR_1.52.0.tar.gz
StartedAt: 2024-12-20 04:36:13 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:36:33 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 20.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RCASPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RCASPAR_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RCASPAR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RCASPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCASPAR’ version ‘1.52.0’
* 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 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 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
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.rd:64: Lost braces
    64 | \code{\link{weight_estimator_BLH}}, code{\link{deriv_weight_estimator_BLH_noprior}}
       |                                         ^
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RCASPAR.Rcheck/00check.log’
for details.


Installation output

RCASPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RCASPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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
Bergamaschi0.0120.0020.014
RCASPAR-package0.2410.0040.245
STpredictor_BLH0.0290.0000.029
STpredictor_xvBLH0.2600.0020.262
deriv_weight_estimator_BLH0.0020.0000.002
deriv_weight_estimator_BLH_noprior0.0020.0010.001
kmplt0.0020.0000.002
kmplt_svrl0.0050.0000.005
logrnk0.0000.0000.001
pltgamma0.0020.0000.001
pltprior0.0020.0000.002
simpson0.0010.0010.001
survData0.0010.0000.001
survivAURC0.0790.0040.084
survivROC0.0200.0010.020
trapezoid0.0000.0000.001
weight_estimator_BLH000
weight_estimator_BLH_noprior0.0020.0000.002
weights_BLH0.0010.0010.003
weights_xvBLH0.0250.0000.025