search

nuno-agostinho / psichomics

Interactive R package to quantify, analyse and visualise alternative splicing
http://nuno-agostinho.github.io/psichomics/
Other
35 stars 11 forks source link

R.utils::evalWithTimeout() -> withTimeout() #383

Closed HenrikBengtsson closed 5 years ago

HenrikBengtsson commented 5 years ago

Hi. The psichomics package calls evalWithTimeout() of R.utils. This function was deprecated in R.utils 2.6.0 (2017-11-05), which meant it was producing a warning everything it was called. It was then made defunct in R.utils 2.8.0 (2018-08-26), meaning it produced a run-time error.

I'm preparing the release of R.utils 2.9.0 where evalWithTimeout() has been removed. This break your package, i.e. it won't install:

* installing *source* package ‘psichomics’ ...
** libs
g++  -I"/usr/share/R/include" -DNDEBUG  -I"/home/hb/repositories/R.utils/revdep/library/psichomics/Rcpp/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3U0YWo/r-base-3.5.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I"/usr/share/R/include" -DNDEBUG  -I"/home/hb/repositories/R.utils/revdep/library/psichomics/Rcpp/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3U0YWo/r-base-3.5.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c psiFastCalc.cpp -o psiFastCalc.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o psichomics.so RcppExports.o psiFastCalc.o -L/usr/lib/R/lib -lR
installing to /home/hb/repositories/R.utils/revdep/checks/psichomics/new/psichomics.Rcheck/psichomics/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error : object ‘evalWithTimeout’ is not exported by 'namespace:R.utils'
ERROR: lazy loading failed for package ‘psichomics’
* removing ‘/home/hb/repositories/R.utils/revdep/checks/psichomics/new/psichomics.Rcheck/psichomics’

Please update code to call withTimeout() instead. That's all that is needed. withTimeout() has been available since R.utils 2.2.0 (2015-12-09).

It would be particularly useful if you could fix this for the current Bioc version before the upcoming freeze.

Thanks

nuno-agostinho commented 5 years ago

Fixed! Thank you for the heads up, @HenrikBengtsson 😄

HenrikBengtsson commented 5 years ago

Thanks for the quick fix.

HenrikBengtsson commented 5 years ago

Did you push this also to Bioc release?

I see that https://bioconductor.org/packages/3.9/bioc/html/psichomics.html is updated, but not https://bioconductor.org/packages/3.8/bioc/html/psichomics.html. It could be that it takes more than two days but, if not, please consider fixing that too because people will stay on R 3.5.3 for a while and they'll get that version of your package and with R.utils 2.9.0 on CRAN, it will break for them.

nuno-agostinho commented 5 years ago

Did you push this also to Bioc release?

I tried but the 3.8 branch is already frozen with the imminent release of the 3.9 branch... I cannot make changes in that version any more.

HenrikBengtsson commented 5 years ago

Ah.. that's unfortunate. I missed that announcement:

On Mon, Apr 15, 2019, 05:12 Shepherd, Lori wrote:

Today is the last day to commit any changes to the release 3.8 branch.  The branch will be frozen to commits as of 4:45 PM  EST.