Awesome, many thanks Martin for the update! Cheers, Andrzej
On Thu, Jan 19, 2017 at 8:08 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/17/2017 07:15 AM, Andrzej Oleś wrote: > >> Thanks Martin! >> >> I see your point - then I suggest that at least the call to >> `devtools::install` is guarded by a customized more informative error >> massage, something along the lines: >> >> Package 'devtools' missing: please install it (e.g., by a call to >> `install.packages('devtools')`) and re-run your biocLite command. >> > > I've updated the error message in 1.25.3; thanks for the suggestion. > > Martin > > >> >> Cheers, >> Andrzej >> >> On Sat, Jan 14, 2017 at 9:43 AM, Martin Morgan >> <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>> >> >> wrote: >> >> On 01/13/2017 06:29 PM, Andrzej Oleś wrote: >> >> Dear all, >> >> it's great that for some time now `biocLite()` also resolves >> package >> dependencies for GitHub hosted packages. However, as this >> functionality >> depends on devtools, an attempt to install a GitHub package when >> devtools >> is not installed results in an error >> >> library(BiocInstaller) >> biocLite("aoles/RBioFormats") >> >> BioC_mirror: https://bioconductor.org >> Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 >> (2016-10-31). >> Error: package 'devtools' not available: there is no package >> called >> ‘devtools’ >> >> If this is the case, one would typically need to first install >> devtools, >> and rerun the biocLite command. I was wondering whether it would >> make sense >> to modify the behavior such that before attempting to call >> `devtools::install` in >> >> https://github.com/Bioconductor-mirror/BiocInstaller/blob/ >> <https://github.com/Bioconductor-mirror/BiocInstaller/blob/> >> 9965cc72d009bfcae6776a02e5abb94cbd5dd109/R/biocLite.R#L48 >> >> first check for devtools availability and try to automatically >> install it >> if missing (maybe by prompting the user). What do you think? >> >> >> I'm not a fan of automatic package installation, e.g., because a >> user (e.g., me) might have a configuration of library paths that >> they are trying to maintain. This leads me down the slippery slope >> of not wanting to offer to install a package, either, because again >> the offer would be too narrow, some users (again, e.g., me) will >> reject it and prefer to have control, and so why not have a standard >> work flow -- user fixes package installation to their satisfaction >> and tries again -- rather than a conditional work flow. >> >> On the other hand the error message "package 'devtools' not >> available: there is no package called 'devtools'" seems to be poorly >> worded -- there is a package devtools, and it is available, just not >> in the current installation. One could try to provide a better >> message, but one would rather the message were improved upstream so >> all similar situations were handled the same; at least this way the >> user has to learn only once what the message means. >> >> Martin >> >> >> Cheers, >> Andrzej >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> >> >> >> This email message may contain legally privileged and/or >> confidential information. If you are not the intended recipient(s), >> or the employee or agent responsible for the delivery of this >> message to the intended recipient(s), you are hereby notified that >> any disclosure, copying, distribution, or use of this email message >> is prohibited. If you have received this message in error, please >> notify the sender immediately by e-mail and delete this email >> message from your computer. Thank you. >> >> >> > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel