[Bioc-devel] error on R CMD check

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 at 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".

Thanks,
  Zhigang
  https://sites.google.com/view/zlab

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

Hi,

On 06/12/2022 22:10, Herv? Pag?s wrote:
...

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.

This is done. Version 1.1.1 should show up on Friday's build report. 
Hopefully without the BiocGenerics:::testPackage("IFAA") error.

Remember to resync the IFAA repo on GitHub with IFAA's repo on 
git.bioconductor.org

Best,

H.

Best,

H.

Thanks,
? Zhigang
? https://sites.google.com/view/zlab

Hi,

IFAA now passes BUILD and CHECK on all platforms on the BioC 3.17 
build report:

? https://bioconductor.org/checkResults/3.17/bioc-LATEST/IFAA/

The package is now available in BioC 3.17 via BiocManager::install():

? https://bioconductor.org/packages/3.17/IFAA

Except on Windows. But that's because of an issue with an upstream 
package on this platform that will hopefully be resolved soon. (Note 
that BioC 3.17 users can still install the package from source on 
Windows.)

Cheers,

H.

On 07/12/2022 21:54, Herv? Pag?s wrote:

Hi,

On 06/12/2022 22:10, Herv? Pag?s wrote:
...

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.

This is done. Version 1.1.1 should show up on Friday's build report. 
Hopefully without the BiocGenerics:::testPackage("IFAA") error.

Remember to resync the IFAA repo on GitHub with IFAA's repo on 
git.bioconductor.org

Best,

H.

Best,

H.

Thanks,
? Zhigang
? https://sites.google.com/view/zlab