search for: bbsoptions

Dear all, When running R CMD check on my Mac (Yosemite 10.10.5) I get suddenly NOTEs and WARNINGs that my tar.gz file does contain hidden files. However, when checking the corresponding directories with 'ls -al' (or with mc) none of these files does exist!! (with exception .BBSoptions). Here is a partial output of 00check.log: * using log directory '/Volumes/LumiData/CRAN/xps.Rcheck' * using R version 3.2.0 (2015-04-16) * using platform: x86_64-apple-darwin13.4.0 (64-bit) * using session charset: ASCII * checking for file 'xps/DESCRIPTION' ... OK * this is pack...

...tar on Mac OS X, see: http://unix.stackexchange.com/questions/9665/create-tar-archive-of-a-directory-except-for-hidden-files Instead of doing: $tar czf xps_1.29.2.tar.gz xps I did now: $COPYFILE_DISABLE=1 tar czf xps_1.29.2.tar.gz xps Running: $R CMD check xps_1.29.2.tar.gz now leaves only '.BBSoptions' as hidden file. However, I must admit that I do not understand it. Since more than ten years I am running the 'tar' command on my Macs (using Leopard, Snow Leopard, Lion and now Yosemite) and running R CMD check did never give these warning messages. Even two weeks ago everything w...

...> When running R CMD check on my Mac (Yosemite 10.10.5) I get suddenly NOTEs and WARNINGs > that my tar.gz file does contain hidden files. > > However, when checking the corresponding directories with 'ls -al' (or with mc) > none of these files does exist!! (with exception .BBSoptions). > > Here is a partial output of 00check.log: > > * using log directory '/Volumes/LumiData/CRAN/xps.Rcheck' > * using R version 3.2.0 (2015-04-16) > * using platform: x86_64-apple-darwin13.4.0 (64-bit) > * using session charset: ASCII > * checking for file 'xp...

...create-tar-archive-of-a-directory-except-for-hidden-files > | > | Instead of doing: > | $tar czf xps_1.29.2.tar.gz xps > | > | I did now: > | $COPYFILE_DISABLE=1 tar czf xps_1.29.2.tar.gz xps > | > | Running: > | $R CMD check xps_1.29.2.tar.gz > | now leaves only '.BBSoptions' as hidden file. > > No, still wrong. As Simon said, we all are supposed to use 'R CMD build xps' > to create the tarball. "Back in the day ..." straight tar cfz ... worked, it > more or less stopped _many_ years ago. Cf TheOneManualThatMatters: > > 1.3...

...; Yes, I know, however forget for one moment R. > > If I use tar independent of R it still should not create these hidden files. > > BTW, do you know where these hidden files are stored on the Mac? > Please consider reading my original reply - those are not actual files (all but .BBSoptions which is an actual file you can see with ls -a), those are just resource forks of files [or extended attributes in general] -- and Apple tar if instructed to preserve resource forks encodes them as ._* in tar balls since tar has no native way of storing resource forks. And, again, as I said in my r...

...| http://unix.stackexchange.com/questions/9665/create-tar-archive-of-a-directory-except-for-hidden-files | | Instead of doing: | $tar czf xps_1.29.2.tar.gz xps | | I did now: | $COPYFILE_DISABLE=1 tar czf xps_1.29.2.tar.gz xps | | Running: | $R CMD check xps_1.29.2.tar.gz | now leaves only '.BBSoptions' as hidden file. No, still wrong. As Simon said, we all are supposed to use 'R CMD build xps' to create the tarball. "Back in the day ..." straight tar cfz ... worked, it more or less stopped _many_ years ago. Cf TheOneManualThatMatters: 1.3.1 Checking packages -----...

...-for-hidden-files >> | >> | Instead of doing: >> | $tar czf xps_1.29.2.tar.gz xps >> | >> | I did now: >> | $COPYFILE_DISABLE=1 tar czf xps_1.29.2.tar.gz xps >> | >> | Running: >> | $R CMD check xps_1.29.2.tar.gz >> | now leaves only '.BBSoptions' as hidden file. >> >> No, still wrong. As Simon said, we all are supposed to use 'R CMD build xps' >> to create the tarball. "Back in the day ..." straight tar cfz ... worked, it >> more or less stopped _many_ years ago. Cf TheOneManualThatMatters:...

...achine$integer.max for one of the files included in the tarball. This suggests that the resulting tarball might be incorrect. Which is confirmed later when running 'tar ztvf' on that tarball from the Unix comand line: -rw-r--r-- biocbuild/phs_compbio 38 2012-12-11 09:37 ChIPXpressData/.BBSoptions -rw-r--r-- biocbuild/phs_compbio 442 2013-01-18 12:04 ChIPXpressData/DESCRIPTION -rw-r--r-- biocbuild/phs_compbio 0 2012-12-11 09:37 ChIPXpressData/NAMESPACE -rw-r--r-- biocbuild/phs_compbio 14 2012-12-11 09:37 ChIPXpressData/external_data_store.txt drwxr-xr-x biocbuild/phs_compbi...