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proFIA bioncoductor R package
* installing *source* package ‘proFIA’ ...
** using staged installation
** libs
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c UtilFunc.c -o UtilFunc.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-proFIA/00new/proFIA/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, :
The prototype for class “proFIAset” has undefined slot(s): 'fClasses'
Error: unable to load R code in package ‘proFIA’
Execution halted
ERROR: lazy loading failed for package ‘proFIA’
* removing ‘/usr/local/lib/R/site-library/proFIA’
There is no failure on http://bioconductor.org/checkResults/3.8/bioc-LATEST/proFIA/
There is some mismatch between classes
and fClasses` in https://github.com/adelabriere/proFIA/blob/master/R/classContainer.R#L84
Yours, Steffen
Hi,
currently proFIA fails on BioC with an ERROR:
http://bioconductor.org/checkResults/devel/bioc-LATEST/proFIA/malbec1-buildsrc.html
Unfortunately the error message is not very descriptive:
Error: processing vignette 'proFIA-vignette.Rmd' failed with diagnostics:
argument "f" is missing, with no default
--- failed re-building ‘proFIA-vignette.Rmd’
Yours,
Steffen
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