[Rd] Error in gzfile(file, mode) when checking a package with rcmd check
Hi, For the first time I have a strange behaviour when checking a package before 'packaging' the code. Looks like a file cannot be read. rcmd check pgirmess * using log directory 'U:/Documents and Settings/pgiraudo/Mes documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck' * using R version 2.13.2 (2011-09-30) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'pgirmess/DESCRIPTION' ... OK * this is package 'pgirmess' version '1.5.2' * checking package dependencies ... OK * checking if this is a source package ... OK * checking for .dll and .exe files ... OK * checking whether package 'pgirmess' can be installed ... ERROR Installation failed. See 'U:/Documents and Settings/pgiraudo/Mes documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck/00install.out' for details. In '00install.out', I get: * installing *source* package 'pgirmess' ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in gzfile(file, mode) : cannot open the connection Calls: %in% -> match -> installed.packages -> saveRDS -> gzfile In addition: Warning message: In gzfile(file, mode) : cannot open compressed file 'U:\DOCUME~1\Admin\LOCALS~1\Temp\RtmpwWcmem/libloc_U%3a%2fDocuments%20and%20Settings%2fpgiraudo%2fMes%20documents%2fR%2fpgir_arch%2fpgirmess_arch%2fOn%20work%2fpgirmess.RcheckVersion,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,OS_type,License,Archs,Built.rds', probable reason 'No such file or directory' Execution halted ERROR: loading failed * removing 'U:/DOCUME~1/pgiraudo/MESDOC~1/R/PGIR_A~1/PGIRME~1/ONWORK~1/PGIRME~1.RCH/pgirmess' Any hint welcome ! I am stuck on that. Patrick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error in gzfile(file, mode) when checking a package with rcmd check
PS: looks like if it has something to do with moving from R 2.13.1 to R 2.13.2, since I cannot even check earlier versions of the pgirmess package that where well checked and compiled under earlier R versions. Le 16/10/2011 09:50, Patrick Giraudoux a écrit : Hi, For the first time I have a strange behaviour when checking a package before 'packaging' the code. Looks like a file cannot be read. rcmd check pgirmess * using log directory 'U:/Documents and Settings/pgiraudo/Mes documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck' * using R version 2.13.2 (2011-09-30) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'pgirmess/DESCRIPTION' ... OK * this is package 'pgirmess' version '1.5.2' * checking package dependencies ... OK * checking if this is a source package ... OK * checking for .dll and .exe files ... OK * checking whether package 'pgirmess' can be installed ... ERROR Installation failed. See 'U:/Documents and Settings/pgiraudo/Mes documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck/00install.out' for details. In '00install.out', I get: * installing *source* package 'pgirmess' ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in gzfile(file, mode) : cannot open the connection Calls: %in% -> match -> installed.packages -> saveRDS -> gzfile In addition: Warning message: In gzfile(file, mode) : cannot open compressed file 'U:\DOCUME~1\Admin\LOCALS~1\Temp\RtmpwWcmem/libloc_U%3a%2fDocuments%20and%20Settings%2fpgiraudo%2fMes%20documents%2fR%2fpgir_arch%2fpgirmess_arch%2fOn%20work%2fpgirmess.RcheckVersion,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,OS_type,License,Archs,Built.rds', probable reason 'No such file or directory' Execution halted ERROR: loading failed * removing 'U:/DOCUME~1/pgiraudo/MESDOC~1/R/PGIR_A~1/PGIRME~1/ONWORK~1/PGIRME~1.RCH/pgirmess' Any hint welcome ! I am stuck on that. Patrick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error in gzfile(file, mode) when checking a package with rcmd check
Also have just tried to build the package with no preliminary check. The package apparently builds OK, tar.gz as well as binary .zip. Really looks like the error has to do with the rcmd check command specifically... May it be a bug ? Suppose I am not the only one to have checked a package since R 2.13.2 has been delivered ? Patrick Le 16/10/2011 11:02, Patrick Giraudoux a écrit : PS: looks like if it has something to do with moving from R 2.13.1 to R 2.13.2, since I cannot even check earlier versions of the pgirmess package that where well checked and compiled under earlier R versions. Le 16/10/2011 09:50, Patrick Giraudoux a écrit : Hi, For the first time I have a strange behaviour when checking a package before 'packaging' the code. Looks like a file cannot be read. rcmd check pgirmess * using log directory 'U:/Documents and Settings/pgiraudo/Mes documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck' * using R version 2.13.2 (2011-09-30) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'pgirmess/DESCRIPTION' ... OK * this is package 'pgirmess' version '1.5.2' * checking package dependencies ... OK * checking if this is a source package ... OK * checking for .dll and .exe files ... OK * checking whether package 'pgirmess' can be installed ... ERROR Installation failed. See 'U:/Documents and Settings/pgiraudo/Mes documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck/00install.out' for details. In '00install.out', I get: * installing *source* package 'pgirmess' ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in gzfile(file, mode) : cannot open the connection Calls: %in% -> match -> installed.packages -> saveRDS -> gzfile In addition: Warning message: In gzfile(file, mode) : cannot open compressed file 'U:\DOCUME~1\Admin\LOCALS~1\Temp\RtmpwWcmem/libloc_U%3a%2fDocuments%20and%20Settings%2fpgiraudo%2fMes%20documents%2fR%2fpgir_arch%2fpgirmess_arch%2fOn%20work%2fpgirmess.RcheckVersion,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,OS_type,License,Archs,Built.rds', probable reason 'No such file or directory' Execution halted ERROR: loading failed * removing 'U:/DOCUME~1/pgiraudo/MESDOC~1/R/PGIR_A~1/PGIRME~1/ONWORK~1/PGIRME~1.RCH/pgirmess' Any hint welcome ! I am stuck on that. Patrick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] trace an Rd conversion error in R cmd check
Hi.
On Wed, Oct 12, 2011 at 9:24 AM, Joshua Wiley wrote:
> Hi All,
>
> Apologies if this is a very naive question. Is there a way to see the
> particular Rd file being processed right before a warning/error
> occurs? As far as I can tell, all my .Rd files use have names and
> titles and they are unique between Rd files (sometimes in a file I use
> something like \name{foo} \title{Foo}). I seem to be able to convert
> files to latex using: R CMD Rdconv --type=latex on all my Rd files
> without problems.
>
> Here is the warning and error:
>
> * checking PDF version of manual ... ERROR
> Rd conversion errors:
> Warning in file(con, "r") :
> file("") only supports open = "w+" and open = "w+b": using the former
> Error : : Sections \title, and \name must exist and be unique in Rd files
For what it is worth: I also get this error when I try to "R CMD
check" any of my many packages on R Under development (unstable)
(2011-10-13 r57231) on Windows 7. It does not occur with R version
2.14.0 alpha (2011-10-14 r57245). I haven't had time to troubleshoot
this and I figured I'll wait a few revisions.
The error does not occur when using tools::checkRd(), e.g.
> setwd("R.methodsS3/man/");
> filenames <- list.files(pattern="[.]Rd$");
> dummy <- sapply(pathnames, FUN=tools::checkRd);
>
/Henrik
>
> I am using:
>
> R Under development (unstable) (2011-10-11 r57214)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> on Windows 7 with Rtools 2.14 and MikTeX 2.9
>
> Any suggestions or pointers to manuals/documentation would be greatly
> appreciated.
>
> Thanks,
>
> Josh
>
>
> --
> Joshua Wiley
> Ph.D. Student, Health Psychology
> Programmer Analyst II, ATS Statistical Consulting Group
> University of California, Los Angeles
> https://joshuawiley.com/
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
__
R-devel@r-project.org mailing list
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Re: [Rd] Error in gzfile(file, mode) when checking a package with rcmd check
Hmm, I have not had any difficulty with 2.13.2 on x86_64-pc-mingw32/x64, but I do have trouble with R CMD check on R devel, as has another user now. It is never with building or installing, just the checking. In my case, the error comes when building the manual. 2011/10/16 Patrick Giraudoux : > Also have just tried to build the package with no preliminary check. The > package apparently builds OK, tar.gz as well as binary .zip. Really looks > like the error has to do with the rcmd check command specifically... May it > be a bug ? Suppose I am not the only one to have checked a package since R > 2.13.2 has been delivered ? > > Patrick > > > Le 16/10/2011 11:02, Patrick Giraudoux a écrit : >> >> PS: looks like if it has something to do with moving from R 2.13.1 to R >> 2.13.2, since I cannot even check earlier versions of the pgirmess package >> that where well checked and compiled under earlier R versions. >> >> >> Le 16/10/2011 09:50, Patrick Giraudoux a écrit : >>> >>> Hi, >>> >>> For the first time I have a strange behaviour when checking a package >>> before 'packaging' the code. Looks like a file cannot be read. >>> >>> rcmd check pgirmess >>> >>> * using log directory 'U:/Documents and Settings/pgiraudo/Mes >>> documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck' >>> * using R version 2.13.2 (2011-09-30) >>> * using platform: i386-pc-mingw32 (32-bit) >>> * using session charset: ISO8859-1 >>> * checking for file 'pgirmess/DESCRIPTION' ... OK >>> * this is package 'pgirmess' version '1.5.2' >>> * checking package dependencies ... OK >>> * checking if this is a source package ... OK >>> * checking for .dll and .exe files ... OK >>> * checking whether package 'pgirmess' can be installed ... ERROR >>> Installation failed. >>> See 'U:/Documents and Settings/pgiraudo/Mes >>> documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck/00install.out' >>> for details. >>> >>> >>> In '00install.out', I get: >>> >>> * installing *source* package 'pgirmess' ... >>> ** R >>> ** data >>> ** preparing package for lazy loading >>> ** help >>> *** installing help indices >>> ** building package indices ... >>> ** testing if installed package can be loaded Error in gzfile(file, mode) >>> : cannot open the connection >>> Calls: %in% -> match -> installed.packages -> saveRDS -> gzfile >>> In addition: Warning message: >>> In gzfile(file, mode) : >>> cannot open compressed file >>> 'U:\DOCUME~1\Admin\LOCALS~1\Temp\RtmpwWcmem/libloc_U%3a%2fDocuments%20and%20Settings%2fpgiraudo%2fMes%20documents%2fR%2fpgir_arch%2fpgirmess_arch%2fOn%20work%2fpgirmess.RcheckVersion,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,OS_type,License,Archs,Built.rds', >>> probable reason 'No such file or directory' >>> Execution halted >>> ERROR: loading failed >>> * removing >>> 'U:/DOCUME~1/pgiraudo/MESDOC~1/R/PGIR_A~1/PGIRME~1/ONWORK~1/PGIRME~1.RCH/pgirmess' >>> >>> Any hint welcome ! I am stuck on that. >>> >>> Patrick >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
