Multiple platform build/check report for BioC 3.21 - CHECK results for CFAssay on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4349
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*

CHECK results for CFAssay on nebbiolo1

To the developers/maintainers of the CFAssay package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CFAssay.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: CFAssay

Version: 1.41.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CFAssay.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CFAssay_1.41.0.tar.gz

StartedAt: 2024-11-24 21:07:38 -0500 (Sun, 24 Nov 2024)

EndedAt: 2024-11-24 21:11:39 -0500 (Sun, 24 Nov 2024)

EllapsedTime: 241.2 seconds

RetCode: 0

Status: OK

CheckDir: CFAssay.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CFAssay.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CFAssay_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CFAssay.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘CFAssay/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CFAssay’ version ‘1.41.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘CFAssay’ 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 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
cellsurvLQdiff : fitLQ.MLdiff: no visible global function definition
  for ‘glm’
cellsurvLQdiff : fitLQ.MLdiff: no visible global function definition
  for ‘quasipoisson’
cellsurvLQdiff : fitLQ.MLdiff: no visible global function definition
  for ‘anova’
cellsurvLQdiff : fitLQ.LSdiff: no visible global function definition
  for ‘lm’
cellsurvLQdiff : fitLQ.LSdiff: no visible global function definition
  for ‘anova’
cellsurvLQdiff : fitLQ1.MLdiff: no visible global function definition
  for ‘glm’
cellsurvLQdiff : fitLQ1.MLdiff: no visible global function definition
  for ‘quasipoisson’
cellsurvLQdiff : fitLQ1.MLdiff: no visible global function definition
  for ‘anova’
cellsurvLQdiff : fitLQ1.LSdiff: no visible global function definition
  for ‘lm’
cellsurvLQdiff : fitLQ1.LSdiff: no visible global function definition
  for ‘anova’
cellsurvLQdiff : fitLQ1.LSdiffFr: no visible global function definition
  for ‘lm’
cellsurvLQdiff : fitLQ1.LSdiffFr: no visible global function definition
  for ‘anova’
cellsurvLQfit : fitLQ.ML: no visible global function definition for
  ‘glm’
cellsurvLQfit : fitLQ.ML: no visible global function definition for
  ‘quasipoisson’
cellsurvLQfit : fitLQ.LS: no visible global function definition for
  ‘lm’
cellsurvLQfit : fitLQ1.ML: no visible global function definition for
  ‘glm’
cellsurvLQfit : fitLQ1.ML: no visible global function definition for
  ‘quasipoisson’
cellsurvLQfit : fitLQ1.LS: no visible global function definition for
  ‘lm’
cellsurvLQfit : fitLQ1.LSfr: no visible global function definition for
  ‘lm’
cfa2way: no visible global function definition for ‘formula’
cfa2way: no visible global function definition for ‘glm’
cfa2way: no visible global function definition for ‘quasipoisson’
cfa2way: no visible global function definition for ‘anova’
cfa2way: no visible global function definition for ‘lm’
pes : <anonymous>: no visible global function definition for ‘glm’
pes : <anonymous>: no visible global function definition for
  ‘quasipoisson’
pes : <anonymous>: no visible global function definition for ‘lm’
pes : <anonymous>: no visible binding for global variable ‘logPle’
plot.cellsurvLQfit: no visible global function definition for ‘par’
plot.cellsurvLQfit: no visible global function definition for ‘curve’
plot.cellsurvLQfit: no visible global function definition for ‘points’
plot.cellsurvLQfit: no visible global function definition for
  ‘segments’
plotExp.cellsurvLQfit: no visible global function definition for ‘par’
plotExp.cellsurvLQfit: no visible global function definition for ‘glm’
plotExp.cellsurvLQfit: no visible global function definition for
  ‘quasipoisson’
plotExp.cellsurvLQfit: no visible global function definition for
  ‘segments’
plotExp.cellsurvLQfit: no visible global function definition for
  ‘curve’
plotExp.cellsurvLQfit: no visible global function definition for
  ‘legend’
plotExp.cellsurvLQfit: no visible global function definition for ‘text’
plotExp.cellsurvLQfit: no visible global function definition for
  ‘title’
plotExp.cellsurvLQfit: no visible global function definition for ‘lm’
plotExp.cfa2way: no visible global function definition for ‘par’
plotExp.cfa2way: no visible global function definition for ‘barplot’
plotExp.cfa2way: no visible global function definition for ‘points’
plotExp.cfa2way: no visible global function definition for ‘segments’
plotExp.cfa2way: no visible global function definition for ‘text’
plotExp.cfa2way: no visible global function definition for ‘title’
plotExp.cfa2way: no visible global function definition for ‘box’
sfpmean : sf.mean: no visible global function definition for ‘glm’
sfpmean : sf.mean: no visible global function definition for
  ‘quasipoisson’
sfpmean : sf.mean: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  anova barplot box curve formula glm legend lm logPle par points
  poisson quasipoisson segments text title
Consider adding
  importFrom("graphics", "barplot", "box", "curve", "legend", "par",
             "points", "segments", "text", "title")
  importFrom("stats", "anova", "formula", "glm", "lm", "poisson",
             "quasipoisson")
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 installed files from ‘inst/doc’ ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CFAssay.Rcheck/00check.log’
for details.

Installation output

CFAssay.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CFAssay
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CFAssay’ ...
** using staged installation
** R
** inst
** 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 (CFAssay)

Tests output

Example timings

CFAssay.Rcheck/CFAssay-Ex.timings

name	user	system	elapsed
cellsurvLQdiff	0.163	0.014	0.178
cellsurvLQfit	0.029	0.004	0.032
cfa2way	0.020	0.003	0.024
pes	0.032	0.002	0.033
plot.cellsurvLQfit	0.156	0.000	0.157
plotExp	0.047	0.001	0.049
plotExp.cellsurvLQfit	0.050	0.002	0.051
plotExp.cfa2way	0.028	0.002	0.028
plotExp.default	0.047	0.001	0.049
print.cellsurvLQdiff	0.044	0.006	0.051
print.cellsurvLQfit	0.026	0.002	0.027
print.cfa2way	0.011	0.001	0.011
sfpmean	0.052	0.000	0.054