[Bioc-devel] error on R CMD check

[Hervé Pagès]

Hi,

On 06/12/2022 21:01, Zhigang Li wrote:
> Dear Bioconductor Developers,
>
> Can you please help with an error message from R CMD check for the package IFAA?
>
> The BioConductor platform produced the following error message when
> running R CMD check
> (http://bioconductor.org/checkResults/devel/bioc-LATEST/IFAA/nebbiolo1-checksrc.html):
>    "
>    BiocGenerics:::testPackage("IFAA")
>    Error in BiocGenerics:::testPackage("IFAA") :
>      unable to find unit tests, no subdir 'unitTests'
>    Execution halted
>    "
>
>    However, the error is very strange because the subdirectory
>   "unitTests" is there in the folder "inst". And we have previously
>   passed the test of the package thru the github webpage
>   (https://github.com/Bioconductor/Contributions/issues/2651). We have
>   also tested it on our own computer and it did not have this error.
> Below is the output from our personal computer.
>
> (base) quranwu using MacBook-Pro-4 test % R CMD check --library=./
> --no-vignettes --timings IFAA_0.99.9.tar.gz
> * using log directory ‘/Users/quranwu/Desktop/test/IFAA.Rcheck’
> * using R version 4.2.1 (2022-06-23)
> * using platform: x86_64-apple-darwin17.0 (64-bit)
> * using session charset: UTF-8
> * using option ‘--no-vignettes’
> * checking for file ‘IFAA/DESCRIPTION’ ... OK
> * this is package ‘IFAA’ version ‘0.99.9’
> * 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 executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package ‘IFAA’ 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 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 ... OK
> * 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 sizes of PDF files under ‘inst/doc’ ... OK
> * checking installed files from ‘inst/doc’ ... OK
> * checking files in ‘vignettes’ ... OK
> * checking examples ... OK
> Examples with CPU (user + system) or elapsed time > 5s
>          user system elapsed
> IFAA  12.723  0.146  72.684
> MZILN  0.944  0.020  15.038
> * checking for unstated dependencies in ‘tests’ ... OK
> * checking tests ...
>    Running ‘runTests.R’
>   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: OK
>
> By any chance could it be because the IFAA package on CRAN got called
> when running BiocGenerics:::testPackage("IFAA") on the BioConductor
> platform? The IFAA package on CRAN indeed does not have the
> subdirectory of "unitTests".

Probably. At the root of the problem is the fact that the IFAA package 
on CRAN is at version 1.1.0 but was submitted to Bioconductor with 
version 0.99.z. When a CRAN package is submitted to Bioconductor, it 
doesn't make sense to reset the version to 0.99.z. More generally 
speaking, package versions should **never** go down because this 
introduces all kinds of problems.

For example, even if the IFAA package in Bioconductor somehow managed to 
pass 'R CMD check' and propagate to the Bioconductor repos, users would 
be unable to install it because BiocManager::install("IFAA") would pick 
up the higher version. And even if a user was somehow able to install 
it, it would be very quickly replaced with the CRAN version the next 
time the user updates their packages (something users and developers 
should do on a regular basis by calling BiocManager::install() with no 
arguments).

What is happening exactly on the build machines with 
BiocGenerics:::testPackage("IFAA") is a slightly more sophisticated 
variant of that.

Anyways, the version of the Bioconductor package would need to be bumped 
to 1.1.1. However you won't be able to push this bump to 
git.bioconductor.org because we don't allow this kind of version bump. 
So we'll take care of it. We'll let you know when it's done.

Best,

H.


> Thanks,
>   Zhigang
>   https://sites.google.com/view/zlab
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com