Re: [R-pkg-devel] Note: significantly better compression could be obtained ...
On Thu, 4 Mar 2021 12:09:51 +0100 Sebastian Meyer wrote: > Am 04.03.21 um 10:24 schrieb Rolf Turner: > > But this still leaves the question: Why the is > > R CMD check telling me to use the flag --resave-data, when I *just > > did that*??? > > Yes, indeed! I've investigated further and found that in R 4.0.0-4.0.4 > the --resave-data option of R CMD build was ineffective for packages > using LazyData. This bug has recently been fixed in R-devel (c79573) > and I think the fix should also be ported to R-patched and appear in > the NEWS. > > Thank you for reporting! Ta-da!!! So I'm not going mad after all!!! :-) Thanks very much for invetools::resaveRdaFiles(),stigating and reassuring me. Thanks also for pointing out the tools::resaveRdaFiles() workaround which provided an interim fix for the problem. cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Note: significantly better compression could be obtained ...
Am 04.03.21 um 10:24 schrieb Rolf Turner: > > On Thu, 4 Mar 2021 08:44:31 +0100 > Sebastian Meyer wrote: > >> Am 04.03.21 um 01:41 schrieb Rolf Turner: >>> >>> ... by using R CMD build --resave-data >>> >>> But I *did* use that flag with my build command!!! And yet "R CMD >>> check" seems to think that I didn't! >> >> Just to be sure: Are you running R CMD check on that freshly built >> tarball or is devtools::check() involved? > > The former. I have never used devtools::check(). >> >>> >>> I have done "R CMD build --resave-data kanova" (where "kanova" is >>> the name of the package in question), to make sure that I didn't >>> fumble-finger somewhere, but there's no change. I always get that >>> NOTE. >>> >>> How on earth can I track down what's going wrong? >> >> - Does the R CMD build log actually show "re-saving image files" or >> "re-saving sysdata.rda"? > > Dunno what you mean by the "R CMD build log". I could grepped > "re-saving" on all files and came up empty handed. I meant the standard output of R CMD build. With --resave-data, it should show something like * checking for empty or unneeded directories * re-saving image files * building '.tar.gz' > >> - Have you set the BuildResaveData field in your DESCRIPTION file? > > No. > >> This would take precedence over the --resave-data command line switch. >> >> - Have you tried running ) on your source data >> directory before building the package? Does that reduce the size of >> your data files? > > Never heard of that. Tried it just now and it reduced the size from > 285607 bytes to 161743 bytes. That's substantial I guess. > > > >> You'll get the NOTE when R CMD check finds that running >> tools::resaveRdaFiles() on the data directory would reduce a file's >> size by more than 10% with a different type of compression (if the >> original size is >10KB). > > Now that I have applied tools::resaveRdaFiles(), I no longer get > the NOTE from R CMD check. So I guess my problem is solved. Thanks. > > But this still leaves the question: Why the is > R CMD check telling me to use the flag --resave-data, when I *just did > that*??? Yes, indeed! I've investigated further and found that in R 4.0.0-4.0.4 the --resave-data option of R CMD build was ineffective for packages using LazyData. This bug has recently been fixed in R-devel (c79573) and I think the fix should also be ported to R-patched and appear in the NEWS. Thank you for reporting! Best regards, Sebastian > > cheers, > > Rolf > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Note: significantly better compression could be obtained ...
On Thu, 4 Mar 2021 08:44:31 +0100 Sebastian Meyer wrote: > Am 04.03.21 um 01:41 schrieb Rolf Turner: > > > > ... by using R CMD build --resave-data > > > > But I *did* use that flag with my build command!!! And yet "R CMD > > check" seems to think that I didn't! > > Just to be sure: Are you running R CMD check on that freshly built > tarball or is devtools::check() involved? The former. I have never used devtools::check(). > > > > > I have done "R CMD build --resave-data kanova" (where "kanova" is > > the name of the package in question), to make sure that I didn't > > fumble-finger somewhere, but there's no change. I always get that > > NOTE. > > > > How on earth can I track down what's going wrong? > > - Does the R CMD build log actually show "re-saving image files" or > "re-saving sysdata.rda"? Dunno what you mean by the "R CMD build log". I could grepped "re-saving" on all files and came up empty handed. > - Have you set the BuildResaveData field in your DESCRIPTION file? No. > This would take precedence over the --resave-data command line switch. > > - Have you tried running ) on your source data > directory before building the package? Does that reduce the size of > your data files? Never heard of that. Tried it just now and it reduced the size from 285607 bytes to 161743 bytes. That's substantial I guess. > You'll get the NOTE when R CMD check finds that running > tools::resaveRdaFiles() on the data directory would reduce a file's > size by more than 10% with a different type of compression (if the > original size is >10KB). Now that I have applied tools::resaveRdaFiles(), I no longer get the NOTE from R CMD check. So I guess my problem is solved. Thanks. But this still leaves the question: Why the is R CMD check telling me to use the flag --resave-data, when I *just did that*??? cheers, Rolf -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Note: significantly better compression could be obtained ...
Am 04.03.21 um 01:41 schrieb Rolf Turner: > > ... by using R CMD build --resave-data > > But I *did* use that flag with my build command!!! And yet "R CMD > check" seems to think that I didn't! Just to be sure: Are you running R CMD check on that freshly built tarball or is devtools::check() involved? > > I have done "R CMD build --resave-data kanova" (where "kanova" is > the name of the package in question), to make sure that I didn't > fumble-finger somewhere, but there's no change. I always get that > NOTE. > > How on earth can I track down what's going wrong? - Does the R CMD build log actually show "re-saving image files" or "re-saving sysdata.rda"? - Have you set the BuildResaveData field in your DESCRIPTION file? This would take precedence over the --resave-data command line switch. - Have you tried running tools::resaveRdaFiles() on your source data directory before building the package? Does that reduce the size of your data files? > > There is only one file "stomata.rda" in kanova/data. The > file was created using: > > save(stomata,file="stomata.rda",version=2) > > The file stomata.rda is a *bit* on the large size; 285607 bytes > according to "ls -l", 279Kb according to the NOTE from R CMD check. > But that's not all that big, is it? And anyway I *did* ask > R CMD build to re-save it! You'll get the NOTE when R CMD check finds that running tools::resaveRdaFiles() on the data directory would reduce a file's size by more than 10% with a different type of compression (if the original size is >10KB). Hope this helps. Best regards, Sebastian Meyer > > When I load stomata.rda, object.size() says that stomata uses 1611312 bytes > of memory. > > I'm running Ubuntu 20.04.2 and R version 4.0.4. > > Has anyone else ever been confronted with this bizarre phenomenon? > > Thanks for any tips. > > cheers, > > Rolf Turner > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Note: significantly better compression could be obtained ...
... by using R CMD build --resave-data But I *did* use that flag with my build command!!! And yet "R CMD check" seems to think that I didn't! I have done "R CMD build --resave-data kanova" (where "kanova" is the name of the package in question), to make sure that I didn't fumble-finger somewhere, but there's no change. I always get that NOTE. How on earth can I track down what's going wrong? There is only one file "stomata.rda" in kanova/data. The file was created using: save(stomata,file="stomata.rda",version=2) The file stomata.rda is a *bit* on the large size; 285607 bytes according to "ls -l", 279Kb according to the NOTE from R CMD check. But that's not all that big, is it? And anyway I *did* ask R CMD build to re-save it! When I load stomata.rda, object.size() says that stomata uses 1611312 bytes of memory. I'm running Ubuntu 20.04.2 and R version 4.0.4. Has anyone else ever been confronted with this bizarre phenomenon? Thanks for any tips. cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
