Re: [R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems
Marc Schwartz (via MN) writes: On Tue, 2006-09-19 at 22:16 +1000, Robert King wrote: Here is another thing that might help work out what is happening. If I use --no-install, ade4 actually fails as well, in the same way as zipfR. [Desktop]$ R CMD check --no-install ade4 * checking for working latex ... OK * using log directory '/home/rak776/Desktop/ade4.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'ade4/DESCRIPTION' ... OK * this is package 'ade4' version '1.4-1' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR [Desktop]$ R CMD check --no-install zipfR * checking for working latex ... OK * using log directory '/home/rak776/Desktop/zipfR.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR snip Robert, I tried the process last night (my time) using the initial instructions on my FC5 system with: $ R --version R version 2.3.1 Patched (2006-08-06 r38829) Copyright (C) 2006 R Development Core Team I could not replicate the problem. However, this morning, with your additional communication: $ R CMD check --no-install zipfR_0.6-0.tar.gz * checking for working latex ... OK * using log directory '/home/marcs/Downloads/zipfR.Rcheck' * using Version 2.3.1 Patched (2006-08-06 r38829) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking Rd files ... OK * checking Rd cross-references ... WARNING Warning in grep(pattern, x, ignore.case, extended, value, fixed, useBytes) : input string 70 is invalid in this locale * checking for missing documentation entries ... WARNING Warning in grep(pattern, x, ignore.case, extended, value, fixed, useBytes) : input string 70 is invalid in this locale All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking DVI version of manual ... OK WARNING: There were 2 warnings, see /home/marcs/Downloads/zipfR.Rcheck/00check.log for details So I am wondering if this raises the possibility of a locale issue on your FC5 system resulting in a problem reading DESCRIPTION files? It may be totally unrelated, but one never knows I suppose. Mine is: $ locale LANG=en_US.UTF-8 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=en_US.UTF-8 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 LC_ALL= HTH, Marc Schwartz That's a bug in tools:::Rd_aliases (it needs to preprocess the Rd lines, which re-encodes if necessary and possible). I'll commit a fix later today. Thanks for spotting this. Best -k __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems
On Wed, 2006-09-20 at 13:20 +0200, Kurt Hornik wrote: Marc Schwartz (via MN) writes: On Tue, 2006-09-19 at 22:16 +1000, Robert King wrote: Here is another thing that might help work out what is happening. If I use --no-install, ade4 actually fails as well, in the same way as zipfR. [Desktop]$ R CMD check --no-install ade4 * checking for working latex ... OK * using log directory '/home/rak776/Desktop/ade4.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'ade4/DESCRIPTION' ... OK * this is package 'ade4' version '1.4-1' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR [Desktop]$ R CMD check --no-install zipfR * checking for working latex ... OK * using log directory '/home/rak776/Desktop/zipfR.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR snip Robert, I tried the process last night (my time) using the initial instructions on my FC5 system with: $ R --version R version 2.3.1 Patched (2006-08-06 r38829) Copyright (C) 2006 R Development Core Team I could not replicate the problem. However, this morning, with your additional communication: $ R CMD check --no-install zipfR_0.6-0.tar.gz * checking for working latex ... OK * using log directory '/home/marcs/Downloads/zipfR.Rcheck' * using Version 2.3.1 Patched (2006-08-06 r38829) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking Rd files ... OK * checking Rd cross-references ... WARNING Warning in grep(pattern, x, ignore.case, extended, value, fixed, useBytes) : input string 70 is invalid in this locale * checking for missing documentation entries ... WARNING Warning in grep(pattern, x, ignore.case, extended, value, fixed, useBytes) : input string 70 is invalid in this locale All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking DVI version of manual ... OK WARNING: There were 2 warnings, see /home/marcs/Downloads/zipfR.Rcheck/00check.log for details So I am wondering if this raises the possibility of a locale issue on your FC5 system resulting in a problem reading DESCRIPTION files? It may be totally unrelated, but one never knows I suppose. Mine is: $ locale LANG=en_US.UTF-8 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=en_US.UTF-8 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 LC_ALL= HTH, Marc Schwartz That's a bug in tools:::Rd_aliases (it needs to preprocess the Rd lines, which re-encodes if necessary and possible). I'll commit a fix later today. Thanks for spotting this. Best -k Thanks for noting this Kurt! Regards, Marc __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems
Robert King [EMAIL PROTECTED] writes: I'm testing a FC5 machine for use in a student lab. R 2.3.1 is installed and seems to work fine. There is one peculiarity - the logins are authenticating to a server, and a verbose flag is set somewhere, leading to lots of spurious messages like this request done: ld 0xa227598 msgid 1 which may be confusing R. However, R CMD check seems to fail for packages with no dependencies at the dependencies check stage. I've tried this with two packages, my own gld and also zipfR. Both fail in the same way. [Desktop]$ R CMD check zipfR_0.6-0.tar.gz * checking for working latex ... OK request done: ld 0x8dfb170 msgid 1 request done: ld 0x8dfb170 msgid 2 * using log directory '/home/rak776/Desktop/zipfR.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking package dependencies ... ERROR [Desktop]$ R CMD check gld * checking for working latex ... OK * using log directory '/home/rak776/Desktop/gld.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'gld/DESCRIPTION' ... OK * this is package 'gld' version '1.8' * checking package dependencies ... ERROR Both these work on two other systems - one a debian/sarge AMD64 and a debian/sarge i386 And at least the former is quite happy on a vanilla FC5/ R2.3.1 What happens if you fire up R --quiet and submit tools:::.check_package_depends(zipfR) (after unpacking the tarball, of course)? This gives no output for me. A package with dependencies checks for dependencies correctly - for example ade4: Desktop]$ R CMD check ade4_1.4-1.tar.gz * checking for working latex ... OK request done: ld 0x994b168 msgid 1 request done: ld 0x994b168 msgid 2 request done: ld 0x994b168 msgid 3 * using log directory '/home/rak776/Desktop/ade4.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'ade4/DESCRIPTION' ... OK * this is package 'ade4' version '1.4-1' * checking package dependencies ... ERROR request done: ld 0xa458598 msgid 1 request done: ld 0xa458598 msgid 2 request done: ld 0xa458598 msgid 3 Packages required but not available: waveslim splancs maptools spdep pixmap ape tripack Does anyone have ideas on what is going wrong? Regards, Robert King -- Robert King, Statistics, School of Mathematical Physical Sciences, University of Newcastle, Australia Room V133 ph +61 2 4921 5548 [EMAIL PROTECTED] http://tolstoy.newcastle.edu.au/~rking/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems
No output from the tools command Peter Dalgaard wrote: Robert King [EMAIL PROTECTED] writes: I'm testing a FC5 machine for use in a student lab. R 2.3.1 is installed and seems to work fine. There is one peculiarity - the logins are authenticating to a server, and a verbose flag is set somewhere, leading to lots of spurious messages like this request done: ld 0xa227598 msgid 1 which may be confusing R. However, R CMD check seems to fail for packages with no dependencies at the dependencies check stage. I've tried this with two packages, my own gld and also zipfR. Both fail in the same way. [Desktop]$ R CMD check zipfR_0.6-0.tar.gz * checking for working latex ... OK request done: ld 0x8dfb170 msgid 1 request done: ld 0x8dfb170 msgid 2 * using log directory '/home/rak776/Desktop/zipfR.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking package dependencies ... ERROR [Desktop]$ R CMD check gld * checking for working latex ... OK * using log directory '/home/rak776/Desktop/gld.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'gld/DESCRIPTION' ... OK * this is package 'gld' version '1.8' * checking package dependencies ... ERROR Both these work on two other systems - one a debian/sarge AMD64 and a debian/sarge i386 And at least the former is quite happy on a vanilla FC5/ R2.3.1 What happens if you fire up R --quiet and submit tools:::.check_package_depends(zipfR) (after unpacking the tarball, of course)? This gives no output for me. Similarly, no output A package with dependencies checks for dependencies correctly - for example ade4: Desktop]$ R CMD check ade4_1.4-1.tar.gz * checking for working latex ... OK request done: ld 0x994b168 msgid 1 request done: ld 0x994b168 msgid 2 request done: ld 0x994b168 msgid 3 * using log directory '/home/rak776/Desktop/ade4.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'ade4/DESCRIPTION' ... OK * this is package 'ade4' version '1.4-1' * checking package dependencies ... ERROR request done: ld 0xa458598 msgid 1 request done: ld 0xa458598 msgid 2 request done: ld 0xa458598 msgid 3 Packages required but not available: waveslim splancs maptools spdep pixmap ape tripack Does anyone have ideas on what is going wrong? Regards, Robert King __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems
Here is another thing that might help work out what is happening. If I use --no-install, ade4 actually fails as well, in the same way as zipfR. [Desktop]$ R CMD check --no-install ade4 * checking for working latex ... OK * using log directory '/home/rak776/Desktop/ade4.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'ade4/DESCRIPTION' ... OK * this is package 'ade4' version '1.4-1' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR [Desktop]$ R CMD check --no-install zipfR * checking for working latex ... OK * using log directory '/home/rak776/Desktop/zipfR.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR Robert King wrote: No output from the tools command Robert King [EMAIL PROTECTED] writes: However, R CMD check seems to fail for packages with no dependencies at the dependencies check stage. I've tried this with two packages, my own gld and also zipfR. Both fail in the same way. [Desktop]$ R CMD check zipfR_0.6-0.tar.gz * checking for working latex ... OK ... * checking package dependencies ... ERROR Both these work on two other systems - one a debian/sarge AMD64 and a debian/sarge i386 And at least the former is quite happy on a vanilla FC5/ R2.3.1 What happens if you fire up R --quiet and submit tools:::.check_package_depends(zipfR) (after unpacking the tarball, of course)? This gives no output for me. Similarly, no output A package with dependencies checks for dependencies correctly - for example ade4: Desktop]$ R CMD check ade4_1.4-1.tar.gz ... Does anyone have ideas on what is going wrong? Regards, Robert King __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems
On Tue, 2006-09-19 at 22:16 +1000, Robert King wrote: Here is another thing that might help work out what is happening. If I use --no-install, ade4 actually fails as well, in the same way as zipfR. [Desktop]$ R CMD check --no-install ade4 * checking for working latex ... OK * using log directory '/home/rak776/Desktop/ade4.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'ade4/DESCRIPTION' ... OK * this is package 'ade4' version '1.4-1' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR [Desktop]$ R CMD check --no-install zipfR * checking for working latex ... OK * using log directory '/home/rak776/Desktop/zipfR.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... ERROR snip Robert, I tried the process last night (my time) using the initial instructions on my FC5 system with: $ R --version R version 2.3.1 Patched (2006-08-06 r38829) Copyright (C) 2006 R Development Core Team I could not replicate the problem. However, this morning, with your additional communication: $ R CMD check --no-install zipfR_0.6-0.tar.gz * checking for working latex ... OK * using log directory '/home/marcs/Downloads/zipfR.Rcheck' * using Version 2.3.1 Patched (2006-08-06 r38829) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking Rd files ... OK * checking Rd cross-references ... WARNING Warning in grep(pattern, x, ignore.case, extended, value, fixed, useBytes) : input string 70 is invalid in this locale * checking for missing documentation entries ... WARNING Warning in grep(pattern, x, ignore.case, extended, value, fixed, useBytes) : input string 70 is invalid in this locale All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking DVI version of manual ... OK WARNING: There were 2 warnings, see /home/marcs/Downloads/zipfR.Rcheck/00check.log for details So I am wondering if this raises the possibility of a locale issue on your FC5 system resulting in a problem reading DESCRIPTION files? It may be totally unrelated, but one never knows I suppose. Mine is: $ locale LANG=en_US.UTF-8 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=en_US.UTF-8 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 LC_ALL= HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems
I'm testing a FC5 machine for use in a student lab. R 2.3.1 is installed and seems to work fine. There is one peculiarity - the logins are authenticating to a server, and a verbose flag is set somewhere, leading to lots of spurious messages like this request done: ld 0xa227598 msgid 1 which may be confusing R. However, R CMD check seems to fail for packages with no dependencies at the dependencies check stage. I've tried this with two packages, my own gld and also zipfR. Both fail in the same way. [Desktop]$ R CMD check zipfR_0.6-0.tar.gz * checking for working latex ... OK request done: ld 0x8dfb170 msgid 1 request done: ld 0x8dfb170 msgid 2 * using log directory '/home/rak776/Desktop/zipfR.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'zipfR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'zipfR' version '0.6-0' * checking package dependencies ... ERROR [Desktop]$ R CMD check gld * checking for working latex ... OK * using log directory '/home/rak776/Desktop/gld.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'gld/DESCRIPTION' ... OK * this is package 'gld' version '1.8' * checking package dependencies ... ERROR Both these work on two other systems - one a debian/sarge AMD64 and a debian/sarge i386 A package with dependencies checks for dependencies correctly - for example ade4: Desktop]$ R CMD check ade4_1.4-1.tar.gz * checking for working latex ... OK request done: ld 0x994b168 msgid 1 request done: ld 0x994b168 msgid 2 request done: ld 0x994b168 msgid 3 * using log directory '/home/rak776/Desktop/ade4.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'ade4/DESCRIPTION' ... OK * this is package 'ade4' version '1.4-1' * checking package dependencies ... ERROR request done: ld 0xa458598 msgid 1 request done: ld 0xa458598 msgid 2 request done: ld 0xa458598 msgid 3 Packages required but not available: waveslim splancs maptools spdep pixmap ape tripack Does anyone have ideas on what is going wrong? Regards, Robert King -- Robert King, Statistics, School of Mathematical Physical Sciences, University of Newcastle, Australia Room V133 ph +61 2 4921 5548 [EMAIL PROTECTED] http://tolstoy.newcastle.edu.au/~rking/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
