Re: [R] R CMD check sh: line 1: make: command not found
On Thu, 26 Jul 2007, David Peltier wrote: hello, I am using R 2.5.0 under OS X. I am having sh: line 1: make: command not found error message when I run R CMD check : Any help would be appreciated. Well, that is easy: 'make' is missing. It should be there in the OS, so you need to talk to your OS support for help in finding/installing it. BTW, the list for MacOS-specific questions if r-sig-mac. R CMD check backtest * checking for working latex ... OK * using log directory '/backtest/trunk/backtest.Rcheck' * using R version 2.5.0 (2007-04-23) * checking for file 'backtest/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'backtest' version '0.2-0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'backtest' can be installed ... 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 non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking data for non-ASCII characters ... OK * creating backtest-Ex.R ... OK * checking examples ... OK * checking tests ... sh: line 1: make: command not found ERROR [[alternative HTML version deleted]] __ 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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 and require() / library() methods
On Wed, 25 Apr 2007, Crispin Miller wrote: Hi, I have a piece of code that decides at runtime whether to load a data package (and which package to load). This is then done with a call to: library(x) (where x is a character variable containing the package name). This causes R CMD check to throw out a warning: 'library' or 'required' calls not declared from: x Which version of R is this? All I can find say 'require'. Does anyone have any suggestions as to a fix or workaround for this? That call should be library(x, character.only=TRUE) and that will in R 2.5.0 stop the warning AFAIK. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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 and require() / library() methods
Many thanks!
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Prof
Brian Ripley
Sent: 25 April 2007 16:03
To: Crispin Miller
Cc: R-help@stat.math.ethz.ch
Subject: Re: [R] R CMD CHECK and require() / library() methods
On Wed, 25 Apr 2007, Crispin Miller wrote:
Hi,
I have a piece of code that decides at runtime whether to
load a data
package (and which package to load).
This is then done with a call to:
library(x)
(where x is a character variable containing the package name).
This causes R CMD check to throw out a warning:
'library' or 'required' calls not declared from:
x
Which version of R is this? All I can find say 'require'.
My mistake - it was a typo it says: 'require'
Does anyone have any suggestions as to a fix or workaround for this?
That call should be
library(x, character.only=TRUE)
and that will in R 2.5.0 stop the warning AFAIK.
It works - much appreciated...
Crispin
This email is confidential and intended solely for the use o...{{dropped}}
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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.
Re: [R] R CMD check error
Christian == Christian Hennig [EMAIL PROTECTED] on Wed, 9 Aug 2006 17:21:18 +0100 (BST) writes: Christian Dear list, R CMD check on my updated package now Christian generated the following error: Christian LaTeX errors when creating DVI version. This Christian typically indicates Rd problems. Christian But the Rd files (and everything else) were Christian checked as OK (I removed the problem about Christian which I asked the list some hours ago, but Christian answers are still appreciated because I rather Christian created a rough workaround than solved it). Christian What can I do to get better information about Christian what caused the problem in my Rd files? Run R CMD Rd2dvi directly on the relevant Rd file. Mit liebem Gruss: Martin __ 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 error (solved)
Thank you Martin,
Christian Dear list, R CMD check on my updated package now
Christian generated the following error:
Christian LaTeX errors when creating DVI version. This
Christian typically indicates Rd problems.
(...)
Run
R CMD Rd2dvi
directly on the relevant Rd file.
This helped me to find the problem (a mathematical formula not using
\eqn{})!
Lieber Gruss zurueck,
Christian
*** --- ***
Christian Hennig
University College London, Department of Statistical Science
Gower St., London WC1E 6BT, phone +44 207 679 1698
[EMAIL PROTECTED], www.homepages.ucl.ac.uk/~ucakche
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Re: [R] R CMD check and RUnit
I have created page [1] in R Wiki on this topic. http://wiki.r-project.org/rwiki/doku.php?id=developers:runit Seth, I have also managed to tweak doRUnit.R so that R CMD check gives an error if the tests fail. I will leave windows port for someone else ;) Gorjanc Gregor [EMAIL PROTECTED] writes: In case you are interested in fusing RUnit with R CMD check under unix alike OS, here is one way of doing/hacking this. My aim was to perform unit tests: (1) during R CMD check (2) at any other time As you know, we've been using the RUnit package in our group here in Seattle to help with the development of Biobase and graph. I've found that writing unit tests improve my coding by making me focus on the API instead of the implementation and by making bug fixing easier. I've been meaning to improve the scripts I use to run the tests and what you've posted is a start in that direction. I have two additional aims, however, that aren't yet covered: (3) R CMD check should give an error if the tests fail. (4) Works on Windows. Lep pozdrav / With regards, Gregor Gorjanc -- University of Ljubljana PhD student Biotechnical FacultyURI: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical Department mail: gregor.gorjanc at bfro.uni-lj.si Groblje 3 tel: +386 (0)1 72 17 861 SI-1230 Domzale fax: +386 (0)1 72 17 888 Slovenia, Europe -- One must learn by doing the thing; for though you think you know it, you have no certainty until you try. Sophocles ~ 450 B.C. __ 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 for packages in a bundle
Hi everyone What you are trying to do does work, I do it all the time, but there are a few details to work out. Because of the above differences I actually generate the DESCRIPTION* files from my Makefile, differently depending on the target. I do too. Having a DESCRIPTION.in is irrelevant: having a Contains: line in DESCRIPTION is the test used. Can we please read the posting guide and not use R-help for 'questions and discussion about code development in R' which is the description of the R-devel list. The posting guide appears to be ambiguous here. If anything, it said to me that R-help was the appropriate list, being The ‘main’ R mailing list, for discussion about problems and solutions using R to solve problems while Questions likely to prompt discussion unintelligible to non- programmers or topics that are too technical for R-help's audience should go to R-devel. I would have said that my bundle problem fell in the first category and not the second: I use the package management features of R to solve problems---and there's no C / C++ in the question. I was just in some confusion about the status of DESCRIPTION.in, which doesn't really count as code development, IMO. Hence R-help. Can we make the which list section of the posting guide more explicit here? I have a similar dilemma for many posts. -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ 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
Re: [R] R CMD check for packages in a bundle
I think you have to remove the DESCRIPTION.in file when you check the
package stand alone. As I recall, if it exists that is the flag to
indicate a bundle. Also beware that the DESCRIPTION file in the stand
alone package is not exactly the same as the DESCRIPTION.in file when it
is part of the bundle.
What you are trying to do does work, I do it all the time, but there are
a few details to work out. Because of the above differences I actually
generate the DESCRIPTION* files from my Makefile, differently depending
on the target.
Paul Gilbert
Robin Hankin wrote:
Hi
[MacOsX 10.4.6; R-2.2.1]
I have a bundle that comprises three packages. I want to run R CMD
check on
each one individually, as it takes a long time to run on all three.
I am
having problems.
The bundle as a whole passes R CMD check, but fails when I cd to the
bundle
directory and run R CMD check on a package directory.
The whole bundle passes:
octopus:~/scratch% R CMD check ./BACCO
* checking for working latex ... OK
* using log directory '/Users/rksh/scratch/BACCO.Rcheck'
* using R version 2.2.1, 2005-12-20
* checking for file 'BACCO/DESCRIPTION' ... OK
* looks like 'BACCO' is a package bundle
* this is bundle 'BACCO' version '1.0-29'
* checking if this is a source bundle ... OK
[snip]
** creating approximator-manual.tex ... OK
** checking approximator-manual.tex ... OK
octopus:~/scratch%
but R CMD check fails on the packages individually:
octopus:~/scratch/BACCO% R CMD check ./calibrator
* checking for working latex ... OK
* using log directory '/Users/rksh/scratch/BACCO/calibrator.Rcheck'
* using R version 2.2.1, 2005-12-20
* checking for file 'calibrator/DESCRIPTION' ... OK
* looks like 'calibrator' is a package bundle
* this is bundle 'BACCO' version '1.0-29'
* checking if this is a source bundle ... OK
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: cd: /
Users/rksh/scratch/BACCO/calibrator/emulator: No such file or directory
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: cd: /
Users/rksh/scratch/BACCO/calibrator/calibrator: No such file or
directory
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: cd: /
Users/rksh/scratch/BACCO/calibrator/approximator: No such file or
directory
ERROR: no 'Package' field in 'DESCRIPTION'
ERROR
Installation failed.
octopus:~/scratch/BACCO%
Both DESCRIPTION and DESCRIPTION.in files seem to be OK:
octopus:~/scratch/BACCO/calibrator% cat DESCRIPTION
Package: calibrator
Description: Performs Bayesian calibration of computer models as per
[snip]
Title: Bayesian calibration of computer models
Bundle: BACCO
Version: 1.0-29
Date: 13 October 2005
Depends: R (= 2.0.0), mvtnorm, adapt
Contains: emulator calibrator approximator
Title: Bayesian Analysis of Computer Code Output
BundleDescription: Bayesian analysis of computer code software. The
bundle contains routines that evaluate the formulae of Kennedy,
O'Hagan, and Oakley.
License: GPL
Author: Robin K. S. Hankin [EMAIL PROTECTED]
Maintainer: Robin K. S. Hankin [EMAIL PROTECTED]
URL: http://www.noc.soton.ac.uk/JRD/SAT/pers/rksh.html
octopus:~/scratch/BACCO/calibrator% cat DESCRIPTION.in
Package: calibrator
Description: Performs Bayesian calibration of computer models as per
[snip]
Title: Bayesian calibration of computer models
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
__
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
La version française suit le texte anglais.
This email may contain privileged and/or confidential inform...{{dropped}}
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Re: [R] R CMD check for packages in a bundle
On Thu, 6 Apr 2006, Paul Gilbert wrote:
I think you have to remove the DESCRIPTION.in file when you check the
package stand alone. As I recall, if it exists that is the flag to
indicate a bundle. Also beware that the DESCRIPTION file in the stand
alone package is not exactly the same as the DESCRIPTION.in file when it
is part of the bundle.
What you are trying to do does work, I do it all the time, but there are
a few details to work out. Because of the above differences I actually
generate the DESCRIPTION* files from my Makefile, differently depending
on the target.
I do too. Having a DESCRIPTION.in is irrelevant: having a Contains: line
in DESCRIPTION is the test used.
Can we please read the posting guide and not use R-help for
'questions and discussion about code development in R'
which is the description of the R-devel list.
Paul Gilbert
Robin Hankin wrote:
Hi
[MacOsX 10.4.6; R-2.2.1]
I have a bundle that comprises three packages. I want to run R CMD
check on
each one individually, as it takes a long time to run on all three.
I am
having problems.
The bundle as a whole passes R CMD check, but fails when I cd to the
bundle
directory and run R CMD check on a package directory.
The whole bundle passes:
octopus:~/scratch% R CMD check ./BACCO
* checking for working latex ... OK
* using log directory '/Users/rksh/scratch/BACCO.Rcheck'
* using R version 2.2.1, 2005-12-20
* checking for file 'BACCO/DESCRIPTION' ... OK
* looks like 'BACCO' is a package bundle
* this is bundle 'BACCO' version '1.0-29'
* checking if this is a source bundle ... OK
[snip]
** creating approximator-manual.tex ... OK
** checking approximator-manual.tex ... OK
octopus:~/scratch%
but R CMD check fails on the packages individually:
octopus:~/scratch/BACCO% R CMD check ./calibrator
* checking for working latex ... OK
* using log directory '/Users/rksh/scratch/BACCO/calibrator.Rcheck'
* using R version 2.2.1, 2005-12-20
* checking for file 'calibrator/DESCRIPTION' ... OK
* looks like 'calibrator' is a package bundle
* this is bundle 'BACCO' version '1.0-29'
* checking if this is a source bundle ... OK
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: cd: /
Users/rksh/scratch/BACCO/calibrator/emulator: No such file or directory
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: cd: /
Users/rksh/scratch/BACCO/calibrator/calibrator: No such file or
directory
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: cd: /
Users/rksh/scratch/BACCO/calibrator/approximator: No such file or
directory
ERROR: no 'Package' field in 'DESCRIPTION'
ERROR
Installation failed.
octopus:~/scratch/BACCO%
Both DESCRIPTION and DESCRIPTION.in files seem to be OK:
octopus:~/scratch/BACCO/calibrator% cat DESCRIPTION
Package: calibrator
Description: Performs Bayesian calibration of computer models as per
[snip]
Title: Bayesian calibration of computer models
Bundle: BACCO
Version: 1.0-29
Date: 13 October 2005
Depends: R (= 2.0.0), mvtnorm, adapt
Contains: emulator calibrator approximator
Title: Bayesian Analysis of Computer Code Output
BundleDescription: Bayesian analysis of computer code software. The
bundle contains routines that evaluate the formulae of Kennedy,
O'Hagan, and Oakley.
License: GPL
Author: Robin K. S. Hankin [EMAIL PROTECTED]
Maintainer: Robin K. S. Hankin [EMAIL PROTECTED]
URL: http://www.noc.soton.ac.uk/JRD/SAT/pers/rksh.html
octopus:~/scratch/BACCO/calibrator% cat DESCRIPTION.in
Package: calibrator
Description: Performs Bayesian calibration of computer models as per
[snip]
Title: Bayesian calibration of computer models
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
__
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
La version française suit le texte anglais.
This email may contain privileged and/or confidential inform...{{dropped}}
__
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
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
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
Re: [R] R CMD check: problems possibly from mapply?
Sorry, just pressing the send button brought the solution :-)
The problem has nothing to do with any programming issues, but rather with
confusion about directories to use R CMD from.
Regards, Ulrike
-- Forwarded Message ---
From: Ulrike Grömping [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Tue, 14 Mar 2006 15:25:05 +0100
Subject: R CMD check: problems possibly from mapply?
Dear expeRts,
I am trying to wrap up a package utilities (for my internal use). After
adding a function datNAtreat that uses mapply, R CMD check gives WARNINGs
for S3 generic/method consistency, checking replacement functions
and checking foreign function calls, all of which are accompanied by the
following error message:
Error in .try_quietly : Error: unable to load R code in
package 'utilities'
Execution halted
Additionally, I get an ERROR for missing documentation entries (which I don't
understand, because this function like all others is documented).
R CMD check works without problems when omitting this function. The function
itself also works when running the code outside the package. I have now
stripped it down (omitted error controls etc., it still works), and can only
guess that the R CMD check problems have to do with mapply (with which I am
not all that familiar).
I include the code (not reproducible) in case someone has an idea what I can
do to make this function packageable. (The function as.factora is defined
elsewhere in the package and takes the arguments x (a column of a data
frame), na.level and na.show (a logical).):
##
datNAtreat - function(x, na.levels=NULL, na.show=FALSE) {
if (!is.data.frame(x)) x - as.data.frame(x)
names - colnames(x)
if (is.null(names)) names - paste(x,1:ncol(x),sep=)
x - as.data.frame(mapply(as.factora, x, na.level=na.levels,
MoreArgs=list(na.show = na.show), SIMPLIFY=FALSE))
colnames(x) - names
return(x)
}
Any suggestions are appreciated, as I have no idea where else to look.
With kind regards, Ulrike
--- End of Forwarded Message ---
**
Prof. Dr. Ulrike Grömping
Fachbereich II
TFH Berlin
Luxemburger Str. 10
13353 Berlin
mail: [EMAIL PROTECTED]
www: www.tfh-berlin.de/~groemp/
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R CMD check barfs at 'suggested' package
R never reloads a package if not asked to, and it is usually users (not R) who `get confused'. Specifying Suggests: multtest just tells 'check' that it needs to be available: it does not tell R to load it. (It also tells install.packages enough to install it if you asked for dependencies to be installed.) This appears to stem from an error in multtest. The example-checking tests (and not R generically) do try to reset the environment after each example, and that includes detaching packages that the example caused to be loaded. Detaching a package does not unload its DLL, but a package's .Last.lib can do so. However, multtest does so incorrectly, via a call to dyn.unload not library.dynam.unload. Namespaces will not help as multtest does not have one (at least in the version I looked at). I suggest R-devel would be a better list for questions about developing packages. (But for now please take this up with multtest maintainer.) On Wed, 1 Feb 2006, Alexander Ploner wrote: I have been running R CMD check for the first time on of our own packages, which otherwise builds, installs and runs just fine. The package depends on package akima and suggests package multtest; suggesting multtest is indicated because a) it loads a lot of other Bioconductor packages, very slowly, and b) it is only needed for one specific subroutine, which executes require(multtest) every time it's called. Now, when I run R CMD check on our package, it terminates when checking the examples in the documentation, claiming that Error in .C(get_stat, as.double(tmp$X), as.integer(tmp$m), as.integer(tmp$n), : C function name not in DLL for package 'multtest' Execution halted A closer look at the output in the -Ex.Rout file shows that this does indeed happen when calling the function mt.teststat in multtest, to which this piece of code belongs. It also shows however, that this only happens in the *second* chunk of example code containing the calling function; before that, three calls to the offending function in the first chunk (ie in a different .Rd file) are executed just fine. Furthermore, if I change the status of multtest from Suggests to Depends in the DESCRIPTION file, R CMD check processes our package without problem. My impression is that R gets confused when re-loading multtest for the second chunk of example code (for what it's worth, the offending .C(get_stat...) does have a PACKAGE argument). My question now: Is there any way of avoiding this problem without loading multtest by default? Would e.g. using a namespace help? If so, how specifically? Etc.? Thanks for your time (and expertise), alexander platform powerpc-apple-darwin7.9.0 arch powerpc os darwin7.9.0 system powerpc, darwin7.9.0 status Patched major2 minor1.0 year 2005 month05 day 12 language R [EMAIL PROTECTED] Medical Epidemiology Biostatistics Karolinska Institutet, Stockholm Tel: ++46-8-524-82329 Fax: ++46-8-31 49 75 [[alternative HTML version deleted]] __ 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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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
Re: [R] R CMD check failure on minimal code
On 8/15/05 5:19 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: Did you remember to declare a dependency on package 'methods'? I suspect not. Please see `Writing R Extensions'. As usual, Professor Ripley, you are correct Thanks, Sean __ 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
Re: [R] R CMD check failure on minimal code
Did you remember to declare a dependency on package 'methods'? I suspect
not. Please see `Writing R Extensions'.
setClass is not part of base R, and those checks are being run with base
R only. I expect your package will not load when R is run with no default
packages. (Quite a few people run R without package 'methods' for
speed, especially on startup -- it takes about half the startup time.)
On Mon, 15 Aug 2005, Sean Davis wrote:
I have a peculiar problem that I'm sure is a simple one, but I can't figure
out what my mistake is. Can someone enlighten me? I have a simple file,
class.R:
##
setClass(abc,representation(a = character, b = ANY))
I have a package directory ExpressCGH1 made with package.skeleton. The
package happily builds and installs, but R CMD check fails with (ignoring
the documenation warnings, etc.):
version
_
platform powerpc-apple-darwin7.9.0
arch powerpc
os darwin7.9.0
system powerpc, darwin7.9.0
status Patched
major2
minor1.1
year 2005
month08
day 12
language R
%%% R CMD check -l '/User
s/sdavis/Library/R/library' ExpressCGH1
* checking for working latex ... OK
* using log directory
'/Users/sdavis/Work/R-Programs/packages/devel/ExpressCGH/E
xpressCGH1.Rcheck'
* using R version 2.1.1, 2005-08-12
* checking for file 'ExpressCGH1/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ExpressCGH1' version '1.0'
* checking if this is a source package ... OK
* Installing *source* package 'ExpressCGH1' ...
** libs
WARNING: no source files found
chmod: /Users/sdavis/Library/R/library/ExpressCGH1/libs/*: No such file or
direc
tory
** R
** help
Building/Updating help pages for package 'ExpressCGH1'
Formats: text html latex example
convertDNAcopyOutput texthtmllatex example
missing link(s): ~~fun~~
** building package indices ...
* DONE (ExpressCGH1)
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Error: unable to load R code in package 'ExpressCGH1'
Call sequence:
2: stop(gettextf(unable to load R code in package '%s',
libraryPkgName(package
)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error: unable to load R code in package 'ExpressCGH1'
Call sequence:
2: stop(gettextf(unable to load R code in package '%s',
libraryPkgName(package
)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error: unable to load R code in package 'ExpressCGH1'
Call sequence:
2: stop(gettextf(unable to load R code in package '%s',
libraryPkgName(package
)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... WARNING
Rd files with likely Rd problems:
Unaccounted top-level text in file
'/Users/sdavis/Work/R-Programs/packages/devel
/ExpressCGH/ExpressCGH1/man/convertDNAcopyOutput.Rd':
Following section 'note':
\n\n ~Make other sections like Warning with \\section{Warning }{}
~\n\n
Rd files with non-standard keywords:
/Users/sdavis/Work/R-Programs/packages/devel/ExpressCGH/ExpressCGH1/man/conv
er
tDNAcopyOutput.Rd:
~kwd1 ~kwd2
Each '\keyword' entry should specify one of the standard keywords (as
listed in file 'KEYWORDS.db' in the 'doc' subdirectory of the R home
directory).
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for missing documentation entries ... ERROR
Error: unable to load R code in package 'ExpressCGH1'
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford
Re: [R] R CMD check failure on minimal code
On 8/15/05, Sean Davis [EMAIL PROTECTED] wrote:
I have a peculiar problem that I'm sure is a simple one, but I can't figure
out what my mistake is. Can someone enlighten me? I have a simple file,
class.R:
##
setClass(abc,representation(a = character, b = ANY))
I have a package directory ExpressCGH1 made with package.skeleton. The
package happily builds and installs, but R CMD check fails with (ignoring
the documenation warnings, etc.):
Can you declare a slot to have class ANY? You can use class ANY
in a method signature but I don't think you can use it for a slot.
Try to see if you can attach the package in R. That may give more
informative errors.
version
_
platform powerpc-apple-darwin7.9.0
arch powerpc
os darwin7.9.0
system powerpc, darwin7.9.0
status Patched
major2
minor1.1
year 2005
month08
day 12
language R
%%% R CMD check -l '/User
s/sdavis/Library/R/library' ExpressCGH1
* checking for working latex ... OK
* using log directory
'/Users/sdavis/Work/R-Programs/packages/devel/ExpressCGH/E
xpressCGH1.Rcheck'
* using R version 2.1.1, 2005-08-12
* checking for file 'ExpressCGH1/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ExpressCGH1' version '1.0'
* checking if this is a source package ... OK
* Installing *source* package 'ExpressCGH1' ...
** libs
WARNING: no source files found
chmod: /Users/sdavis/Library/R/library/ExpressCGH1/libs/*: No such file or
direc
tory
** R
** help
Building/Updating help pages for package 'ExpressCGH1'
Formats: text html latex example
convertDNAcopyOutput texthtmllatex example
missing link(s): ~~fun~~
** building package indices ...
* DONE (ExpressCGH1)
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Error: unable to load R code in package 'ExpressCGH1'
Call sequence:
2: stop(gettextf(unable to load R code in package '%s',
libraryPkgName(package
)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error: unable to load R code in package 'ExpressCGH1'
Call sequence:
2: stop(gettextf(unable to load R code in package '%s',
libraryPkgName(package
)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error: unable to load R code in package 'ExpressCGH1'
Call sequence:
2: stop(gettextf(unable to load R code in package '%s',
libraryPkgName(package
)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... WARNING
Rd files with likely Rd problems:
Unaccounted top-level text in file
'/Users/sdavis/Work/R-Programs/packages/devel
/ExpressCGH/ExpressCGH1/man/convertDNAcopyOutput.Rd':
Following section 'note':
\n\n ~Make other sections like Warning with \\section{Warning }{}
~\n\n
Rd files with non-standard keywords:
/Users/sdavis/Work/R-Programs/packages/devel/ExpressCGH/ExpressCGH1/man/conv
er
tDNAcopyOutput.Rd:
~kwd1 ~kwd2
Each '\keyword' entry should specify one of the standard keywords (as
listed in file 'KEYWORDS.db' in the 'doc' subdirectory of the R home
directory).
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for missing documentation entries ... ERROR
Error: unable to load R code in package 'ExpressCGH1'
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Re: [R] R CMD check doesn't stop with checking examples
Liaw, Andy wrote: One suggestion: After you break the check process, look at the file C:\Gregor\devel\GeneticsPed\GeneticsPed.Rcheck\GeneticsPed-Ex.R and try to see if you can run that in batch mode. You can also look into GeneticsPed-Ex.Rout that tells you where the stuff hangs. Uwe Andy From: Gorjanc Gregor Hello! I am building a package, which includes also one Fortran subroutine, which works fine if I compile it as a shared library and load it into R via dyn.load(). However, when I launch R CMD check it doesn't stop with checking examples. It's just doing and doing ... I pasted the whole output from R CMD check. Does anyone have any suggestions? I'm still using R 2.0.1. C:\Gregor\devel\GeneticsPedRcmd check GeneticsPed * checking for working latex ... OK * using log directory 'C:/Gregor/devel/GeneticsPed/GeneticsPed.Rcheck' * checking for file 'GeneticsPed/DESCRIPTION' ... OK * checking if this is a source package ... OK installing R.css in C:/Gregor/devel/GeneticsPed/GeneticsPed.Rcheck -- Making package GeneticsPed adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... g77 -O2 -Wall -c meuwissen.f -o meuwissen.o ar cr GeneticsPed.a meuwissen.o ranlib GeneticsPed.a gcc --shared -s -o GeneticsPed.dll GeneticsPed.def GeneticsPed.a GeneticsPed_r es.o -Lc:/Programs/R/rw2001/src/gnuwin32 -lg2c -lR ... DLL made installing DLL installing R files installing man source files installing indices installing help Building/Updating help pages for package 'GeneticsPed' Formats: text html latex example chm NAtoUnknown texthtmllatex example code.pedigree texthtmllatex example extend.pedigree texthtmllatex example generate.pedigree texthtmllatex example generationtexthtmllatex example getcode.pedigree texthtmllatex example inbreedingtexthtmllatex example chm is.unknowntexthtmllatex example kinship texthtmllatex example chm pedigree texthtmllatex example chm missing link(s): ?pedigree in kinship? prop.pedigree texthtmllatex example relationshipAdditive texthtmllatex example chm Microsoft HTML Help Compiler 4.74.8702 Compiling c:\Gregor\devel\GeneticsPed\GeneticsPed\chm\GeneticsPed.chm Compile time: 0 minutes, 0 seconds 13 Topics 41 Local links 0 Internet links 1 Graphic Created c:\Gregor\devel\GeneticsPed\GeneticsPed\chm\GeneticsPed.chm, 32,327 byte s Compression decreased file by 10,172 bytes. adding MD5 sums * DONE (GeneticsPed) * checking package directory ... OK * checking for portable file names ... OK * checking package dependencies ... 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 for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C sources/headers ... OK * creating GeneticsPed-Ex.R ... OK * checking examples ... -- Lep pozdrav / With regards, Gregor Gorjanc -- -- University of Ljubljana Biotechnical Faculty URI: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical Departmentemail: gregor.gorjanc at bfro.uni-lj.si Groblje 3 tel: +386 (0)1 72 17 861 SI-1230 Domzalefax: +386 (0)1 72 17 888 Slovenia __ 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 __ 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 __ 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
RE: [R] R CMD check doesn't stop with checking examples
One suggestion: After you break the check process, look at the file C:\Gregor\devel\GeneticsPed\GeneticsPed.Rcheck\GeneticsPed-Ex.R and try to see if you can run that in batch mode. Andy From: Gorjanc Gregor Hello! I am building a package, which includes also one Fortran subroutine, which works fine if I compile it as a shared library and load it into R via dyn.load(). However, when I launch R CMD check it doesn't stop with checking examples. It's just doing and doing ... I pasted the whole output from R CMD check. Does anyone have any suggestions? I'm still using R 2.0.1. C:\Gregor\devel\GeneticsPedRcmd check GeneticsPed * checking for working latex ... OK * using log directory 'C:/Gregor/devel/GeneticsPed/GeneticsPed.Rcheck' * checking for file 'GeneticsPed/DESCRIPTION' ... OK * checking if this is a source package ... OK installing R.css in C:/Gregor/devel/GeneticsPed/GeneticsPed.Rcheck -- Making package GeneticsPed adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... g77 -O2 -Wall -c meuwissen.f -o meuwissen.o ar cr GeneticsPed.a meuwissen.o ranlib GeneticsPed.a gcc --shared -s -o GeneticsPed.dll GeneticsPed.def GeneticsPed.a GeneticsPed_r es.o -Lc:/Programs/R/rw2001/src/gnuwin32 -lg2c -lR ... DLL made installing DLL installing R files installing man source files installing indices installing help Building/Updating help pages for package 'GeneticsPed' Formats: text html latex example chm NAtoUnknown texthtmllatex example code.pedigree texthtmllatex example extend.pedigree texthtmllatex example generate.pedigree texthtmllatex example generationtexthtmllatex example getcode.pedigree texthtmllatex example inbreedingtexthtmllatex example chm is.unknowntexthtmllatex example kinship texthtmllatex example chm pedigree texthtmllatex example chm missing link(s): ?pedigree in kinship? prop.pedigree texthtmllatex example relationshipAdditive texthtmllatex example chm Microsoft HTML Help Compiler 4.74.8702 Compiling c:\Gregor\devel\GeneticsPed\GeneticsPed\chm\GeneticsPed.chm Compile time: 0 minutes, 0 seconds 13 Topics 41 Local links 0 Internet links 1 Graphic Created c:\Gregor\devel\GeneticsPed\GeneticsPed\chm\GeneticsPed.chm, 32,327 byte s Compression decreased file by 10,172 bytes. adding MD5 sums * DONE (GeneticsPed) * checking package directory ... OK * checking for portable file names ... OK * checking package dependencies ... 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 for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C sources/headers ... OK * creating GeneticsPed-Ex.R ... OK * checking examples ... -- Lep pozdrav / With regards, Gregor Gorjanc -- -- University of Ljubljana Biotechnical Faculty URI: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical Departmentemail: gregor.gorjanc at bfro.uni-lj.si Groblje 3 tel: +386 (0)1 72 17 861 SI-1230 Domzalefax: +386 (0)1 72 17 888 Slovenia __ 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 __ 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
Re: [R] R CMD check errors
Chris Jackson wrote:
In my experience these are usually signs of an error in your NAMESPACE
file, such as a function name in the NAMESPACE which does not match the
function name in the package.
If the NAMESPACE is not the problem (is it???) there are several other
points - one has to look closer.
Does the package work properly after INSTALLing it? Is there a filled
./data directory?
Uwe Ligges
Chris
Ollivier TARAMASCO wrote:
I wrote a library which seems to work on my PC, and on different Unix
systems.
As it is written in the Writing R Extensions manual, I execute a R CMD
check on my library.
I have always the same errors messages:
* checking S3 generic/method consistency ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character
.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'TATA'
Execution halted
See section 'Generic functions and methods' of the 'Writing R
Extensions'
manual.
* checking replacement functions ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character
.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'TATA'
Execution halted
In R, the argument of a replacement function which corresponds to the
right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character
.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'TATA'
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
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Re: [R] R CMD check errors
In my experience these are usually signs of an error in your NAMESPACE
file, such as a function name in the NAMESPACE which does not match the
function name in the package.
Chris
Ollivier TARAMASCO wrote:
I wrote a library which seems to work on my PC, and on different Unix
systems.
As it is written in the Writing R Extensions manual, I execute a R CMD
check on my library.
I have always the same errors messages:
* checking S3 generic/method consistency ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character
.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'TATA'
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character
.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'TATA'
Execution halted
In R, the argument of a replacement function which corresponds to the
right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error in .try_quietly({ : Error in library(package, lib.loc = lib.loc,
character
.only = TRUE, verbose = FALSE) :
package/namespace load failed for 'TATA'
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
--
Christopher Jackson [EMAIL PROTECTED], Research Associate,
Department of Epidemiology and Public Health, Imperial College
School of Medicine, Norfolk Place, London W2 1PG, tel. 020 759 43371
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Re: [R] R CMD check testing environment
Ross Boylan wrote:
On Sun, Aug 22, 2004 at 06:58:56PM +0200, Uwe Ligges wrote:
Ross Boylan wrote:
I can't tell from the docs (Writing R Extensions 1.9.1) exactly what
environment the tests, examples, and vignettes that R CMD check tries to
run are in.
In particular:
1) how do I get the package loaded?
2) how do I access data in the data/ directory?
3) where is the material in the other directories? (e.g., has inst/
material been installed? where?)
Apparently (section 1.3) stuff in demo/ is not checked, which seems odd.
By inspecting some other packages, it seems the answer to 1) is that the
package is already loaded, so I don't need to say library(...). In
particular, I don't need to figure out what lib.loc is.
I have some C code as part of the package, so that (well the .so file)
needs to be loaded too.
Yes. You don't need library() in the the help pages' exmaples, but you
need it in tests.
So what should I use for lib.loc?
The default (i.e. you do not need to set it).
2) Others seem to just say data(..), but this doesn't work for me.
I created the data with
save(gold, e2, q2, file=mspath/data/inputs, compress=TRUE)
and later renamed the file to inputs.RData. (check didn't think the
file counted without the extension).
Indeed, the manuals tells us that saved images have to be called either
*.RData (note the capitalization) or *.rda.
I have tried to access it in my test script (under tests/) with both
load and data (e.g., data(inputs), data(inputs.RData),
data(inputs)). I get
data(inputs)
Warning message:
Data set 'inputs' not found in: data(inputs)
Works for me as Mytests.R in Mypackage:
library(Mypackage)
data(MydataInMypackage)
print(MydataInMypackage)
Is this with MydataInMyPackage in the same directory as Mytests.R, or
in data/. I'm attempting the latter.
In ./data, or do you want to use the data for the tests *only*?
For that matter, my assumed answer to 1) doesn't seem to be working out,
because when I try to access one of my functions it tells me it can't
find it. The function name is the same as the package name.
Perhaps the problem is I have inferred answers from \example{}, and the
story for tests/ is different.
Right, see above.
Although I'm currently focussed on running a script in tests/, I'd like
to know what the story is for \examples in documentation or vignettes.
You won't need library() in the examples ...
And it's also unnecessary for vignettes?
I haven't tried it out - why are you not trying it out yourself?
Other people are using library() in vignettes, so I'd just do it as well.
Uwe Ligges
Thanks.
P.S. Is there a typical way to produce the .Rout.save file used in
tests/? What I'm doing is a slightly awkward 2-step process.
Running R CMD check once, looking whether the Rout looks fine (this
should be the step that takes most of the time, and R can't do it for
you), rename the file it, finished.
OK, that's what I was doing.
Uwe Ligges
Thanks.
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Re: [R] R CMD check testing environment
Ross Boylan wrote:
I can't tell from the docs (Writing R Extensions 1.9.1) exactly what
environment the tests, examples, and vignettes that R CMD check tries to
run are in.
In particular:
1) how do I get the package loaded?
2) how do I access data in the data/ directory?
3) where is the material in the other directories? (e.g., has inst/
material been installed? where?)
Apparently (section 1.3) stuff in demo/ is not checked, which seems odd.
By inspecting some other packages, it seems the answer to 1) is that the
package is already loaded, so I don't need to say library(...). In
particular, I don't need to figure out what lib.loc is.
I have some C code as part of the package, so that (well the .so file)
needs to be loaded too.
Yes. You don't need library() in the the help pages' exmaples, but you
need it in tests.
2) Others seem to just say data(..), but this doesn't work for me.
I created the data with
save(gold, e2, q2, file=mspath/data/inputs, compress=TRUE)
and later renamed the file to inputs.RData. (check didn't think the
file counted without the extension).
Indeed, the manuals tells us that saved images have to be called either
*.RData (note the capitalization) or *.rda.
I have tried to access it in my test script (under tests/) with both
load and data (e.g., data(inputs), data(inputs.RData),
data(inputs)). I get
data(inputs)
Warning message:
Data set 'inputs' not found in: data(inputs)
Works for me as Mytests.R in Mypackage:
library(Mypackage)
data(MydataInMypackage)
print(MydataInMypackage)
For that matter, my assumed answer to 1) doesn't seem to be working out,
because when I try to access one of my functions it tells me it can't
find it. The function name is the same as the package name.
Perhaps the problem is I have inferred answers from \example{}, and the
story for tests/ is different.
Right, see above.
Although I'm currently focussed on running a script in tests/, I'd like
to know what the story is for \examples in documentation or vignettes.
You won't need library() in the examples ...
Thanks.
P.S. Is there a typical way to produce the .Rout.save file used in
tests/? What I'm doing is a slightly awkward 2-step process.
Running R CMD check once, looking whether the Rout looks fine (this
should be the step that takes most of the time, and R can't do it for
you), rename the file it, finished.
Uwe Ligges
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Re: [R] R CMD check testing environment
On Sun, Aug 22, 2004 at 06:58:56PM +0200, Uwe Ligges wrote:
Ross Boylan wrote:
I can't tell from the docs (Writing R Extensions 1.9.1) exactly what
environment the tests, examples, and vignettes that R CMD check tries to
run are in.
In particular:
1) how do I get the package loaded?
2) how do I access data in the data/ directory?
3) where is the material in the other directories? (e.g., has inst/
material been installed? where?)
Apparently (section 1.3) stuff in demo/ is not checked, which seems odd.
By inspecting some other packages, it seems the answer to 1) is that the
package is already loaded, so I don't need to say library(...). In
particular, I don't need to figure out what lib.loc is.
I have some C code as part of the package, so that (well the .so file)
needs to be loaded too.
Yes. You don't need library() in the the help pages' exmaples, but you
need it in tests.
So what should I use for lib.loc?
2) Others seem to just say data(..), but this doesn't work for me.
I created the data with
save(gold, e2, q2, file=mspath/data/inputs, compress=TRUE)
and later renamed the file to inputs.RData. (check didn't think the
file counted without the extension).
Indeed, the manuals tells us that saved images have to be called either
*.RData (note the capitalization) or *.rda.
I have tried to access it in my test script (under tests/) with both
load and data (e.g., data(inputs), data(inputs.RData),
data(inputs)). I get
data(inputs)
Warning message:
Data set 'inputs' not found in: data(inputs)
Works for me as Mytests.R in Mypackage:
library(Mypackage)
data(MydataInMypackage)
print(MydataInMypackage)
Is this with MydataInMyPackage in the same directory as Mytests.R, or
in data/. I'm attempting the latter.
For that matter, my assumed answer to 1) doesn't seem to be working out,
because when I try to access one of my functions it tells me it can't
find it. The function name is the same as the package name.
Perhaps the problem is I have inferred answers from \example{}, and the
story for tests/ is different.
Right, see above.
Although I'm currently focussed on running a script in tests/, I'd like
to know what the story is for \examples in documentation or vignettes.
You won't need library() in the examples ...
And it's also unnecessary for vignettes?
Thanks.
P.S. Is there a typical way to produce the .Rout.save file used in
tests/? What I'm doing is a slightly awkward 2-step process.
Running R CMD check once, looking whether the Rout looks fine (this
should be the step that takes most of the time, and R can't do it for
you), rename the file it, finished.
OK, that's what I was doing.
Uwe Ligges
Thanks.
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Re: [R] R CMD check, Windows XP, perl
File::Basename is part of Perl. Your @ING looks wrong (it contains no Perl system directories). Do you have any Perl environmental variables such as PERL5LIB set? On Fri, 4 Jun 2004, TEMPL Matthias wrote: Dear R users and developers, I'm trying to build a package. The R CMD build works fine. The R CMD check produces allways the following error: .. installing indices Can`t locate File/Basename.pm in @ING (@ING contains: D:/../rw1090/share/perl d:/../rw1090/lib .) at D:/../rw1090/share/perl/build-help-windows.pl line 20. BEGIN failed--compilation aborted at D:/../rw1090/share/perl/build-help-windows.pl line 20. Make[2]: *** [indices] Error 2 Make[1] *** [all] Error 2 Make: *** [pkg-myyfunction] Error 2 *** Installation of myyfunction failed *** .. bulid-help-windows.pl at line 20 contains: use File::Basename; library(myyfunction) works, but I have no documentation for my function. The documentation in the man-directory contains \name, \alias, \title, \description and \keyword, which I have filled correctly. I haven't found something to solve my problem in the writing R extensions manual or in the readme.package file. It's a problem with your Perl installation, so try instead your Perl documentation. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R CMD check, latex
It was an (for me not understandable) problem on miktex I´m solving my problem, by copying ..\texmf\miktex\bin\etex.exe to latex.exe I´m wondering that now R CMD check works now. Sorry, for my question to R help. Matthias -Ursprüngliche Nachricht- Von: TEMPL Matthias Gesendet: Freitag, 28. Mai 2004 10:34 An: [EMAIL PROTECTED] Betreff: [R] R CMD check, latex Hello, I'm trying to build a package and the R CMD build works fine. The R CMD check produces an error, because no latex is found. But I have MikTeX installed and it works fine (only?) in combination with WinEdt. After reinstallation of MikTeX (no errors) I have the same problem. I´m not sure if this is a problem of my latex or a problem of the communication from R to my latex. (I´m running R 1.9.0 on Windows XP) I´m really happy if anybody can help me again. Thanks, Matthias __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo /r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R CMD check warning on predict.systemfit
Arne Henningsen wrote: Hi, I added a new function predict.systemfit to our package systemfit to make it closer to other packages (e.g. lm). Now R CMD check complains that the generic function predict has only the argument object, while our function predict.systemfit has more arguments. However, the function predict.lm has also more arguments and they are almost the same as in predict.systemfit. Thus, I think that our way to specify predict.systemfit might be OK in spite of this warning. What should I do? Can I ignore this warning? What will Kurt answer when we submit it ;-) ? Best wishes, Arne Well, you must use object and ... as arguments, but you are allowed to use further arguments. That should not result in a warning. How does your function looks like exactly? Uwe Ligges __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R CMD check warning on predict.systemfit
Hi, thanks, Uwe and Jari, for your helpful comments! Indeed, I forgot the ... argument. R did not exactly say what was wrong. It just said: * checking S3 generic/method consistency ... WARNING predict: function(object, ...) predict.systemfit: function(object, data, se.fit, se.pred, interval, level) and I wrongly assumed that data, se.fit, se.pred, interval shouldn't be there rather than that ... was missing. Thanks again, Arne On Tuesday 16 March 2004 11:14, Jari Oksanen wrote: Arne, Are you sure that R warns about extra variables, or does it warn about missing parameter ...? The syntax of the generic is predict(object, ...) and both these should be in your function. You should have ... even if you do not pass any extra parameters to other functions (been there, seen that). cheers, jari oksanen On Tue, 2004-03-16 at 11:39, Arne Henningsen wrote: Hi, I added a new function predict.systemfit to our package systemfit to make it closer to other packages (e.g. lm). Now R CMD check complains that the generic function predict has only the argument object, while our function predict.systemfit has more arguments. However, the function predict.lm has also more arguments and they are almost the same as in predict.systemfit. Thus, I think that our way to specify predict.systemfit might be OK in spite of this warning. What should I do? Can I ignore this warning? What will Kurt answer when we submit it ;-) ? Best wishes, Arne -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R CMD check errors
On Fri, 12 Mar 2004, Uwe Ligges wrote:
Thomas Stabla wrote:
Hello again,
I tried to isolate the source code, which causes the error messages:
* checking S3 generic/method consistency ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE,
verbose = FALSE) :
package/namespace load failed
* checking for replacement functions with final arg not named 'value'
... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE,
verbose = FALSE) :
package/namespace load failed
I created a new package skeleton by calling package.skeleton(name =
error) from R 1.8.1.
I deleted the subdirectories 'data', 'src' and 'man'.
The NAMESPACE file contains:
exportPattern(^[^\\.])
and lacks:
import(methods)
and for sure you want as well:
exportClass(Parameter)
Thus, the complete file is:
import(methods)
exportClass(Parameter)
exportPattern(^[^\\.])
sounds logical.
BTW, I read Writing R Extensions in HMTL form under Windows R 1.8.1, and
it doesn't mention exportClass.
Also it doesn't describe how to use S4 classes (or package methods) and
namepaces together.
Hence, I think it is not up to date.
The Error.R file in the subdirectory 'R' contains
x - 1
setClass(Parameter, setClass(Parameter, representation(name =
character))
Well, above, you mean:
setClass(Parameter, representation(name = character))
copy paste error, sorry
Now R CMD check distr runs smoothly, thanks for your help.
Thomas Stabla
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Re: [R] R CMD check errors
Thomas Stabla wrote:
On Fri, 12 Mar 2004, Uwe Ligges wrote:
Thomas Stabla wrote:
Hello again,
I tried to isolate the source code, which causes the error messages:
* checking S3 generic/method consistency ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE,
verbose = FALSE) :
package/namespace load failed
* checking for replacement functions with final arg not named 'value'
... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE,
verbose = FALSE) :
package/namespace load failed
I created a new package skeleton by calling package.skeleton(name =
error) from R 1.8.1.
I deleted the subdirectories 'data', 'src' and 'man'.
The NAMESPACE file contains:
exportPattern(^[^\\.])
and lacks:
import(methods)
and for sure you want as well:
exportClass(Parameter)
Thus, the complete file is:
import(methods)
exportClass(Parameter)
exportPattern(^[^\\.])
sounds logical.
BTW, I read Writing R Extensions in HMTL form under Windows R 1.8.1, and
it doesn't mention exportClass.
Also it doesn't describe how to use S4 classes (or package methods) and
namepaces together.
Hence, I think it is not up to date.
You are right, sorry. The version in R-devel (R-1.9.0 alpha) is up to
date and mentions how to handle S4 classes. So you might want to check
that one.
Best,
Uwe
The Error.R file in the subdirectory 'R' contains
x - 1
setClass(Parameter, setClass(Parameter, representation(name =
character))
Well, above, you mean:
setClass(Parameter, representation(name = character))
copy paste error, sorry
Now R CMD check distr runs smoothly, thanks for your help.
Thomas Stabla
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Re: [R] R CMD check errors
Hello again,
I tried to isolate the source code, which causes the error messages:
* checking S3 generic/method consistency ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, character.only =
TRUE, verbose = FALSE) :
package/namespace load failed
* checking for replacement functions with final arg not named 'value' ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, character.only =
TRUE, verbose = FALSE) :
package/namespace load failed
I created a new package skeleton by calling package.skeleton(name =
error) from R 1.8.1.
I deleted the subdirectories 'data', 'src' and 'man'.
The NAMESPACE file contains:
exportPattern(^[^\\.])
The Error.R file in the subdirectory 'R' contains
x - 1
setClass(Parameter, setClass(Parameter, representation(name = character))
This small package produces already the errors mentioned above, if R
CMD check Error is called (R 1.8.1 and also R 1.9.x).
The point is, as soon as I remove the line with the setClass-call,
then R CMD check Error runs without errors (there is a warning about
an empty 'INDEX' file).
If I remove the NAMESPACE file and call R CMD check (after build), I get
these errors:
* checking S3 generic/method consistency ... WARNING
Error in .tryQuietly({ : Error in eval(expr, envir, enclos) : couldn't find function
setClass
Execution halted
* checking for replacement functions with final arg not named 'value' ... WARNING
Error in .tryQuietly({ : Error in eval(expr, envir, enclos) : couldn't find function
setClass
Execution halted
Thanks for your help,
Thomas Stabla
Error directory available at:
http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/Error.tar.gz
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Re: [R] R CMD check errors
Thomas Stabla wrote:
Hello again,
I tried to isolate the source code, which causes the error messages:
* checking S3 generic/method consistency ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, character.only =
TRUE, verbose = FALSE) :
package/namespace load failed
* checking for replacement functions with final arg not named 'value' ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, character.only =
TRUE, verbose = FALSE) :
package/namespace load failed
I created a new package skeleton by calling package.skeleton(name =
error) from R 1.8.1.
I deleted the subdirectories 'data', 'src' and 'man'.
The NAMESPACE file contains:
exportPattern(^[^\\.])
and lacks:
import(methods)
and for sure you want as well:
exportClass(Parameter)
Thus, the complete file is:
import(methods)
exportClass(Parameter)
exportPattern(^[^\\.])
The Error.R file in the subdirectory 'R' contains
x - 1
setClass(Parameter, setClass(Parameter, representation(name = character))
Well, above, you mean:
setClass(Parameter, representation(name = character))
Uwe Ligges
This small package produces already the errors mentioned above, if R
CMD check Error is called (R 1.8.1 and also R 1.9.x).
The point is, as soon as I remove the line with the setClass-call,
then R CMD check Error runs without errors (there is a warning about
an empty 'INDEX' file).
If I remove the NAMESPACE file and call R CMD check (after build), I get
these errors:
* checking S3 generic/method consistency ... WARNING
Error in .tryQuietly({ : Error in eval(expr, envir, enclos) : couldn't find function
setClass
Execution halted
* checking for replacement functions with final arg not named 'value' ... WARNING
Error in .tryQuietly({ : Error in eval(expr, envir, enclos) : couldn't find function
setClass
Execution halted
Thanks for your help,
Thomas Stabla
Error directory available at:
http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/Error.tar.gz
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Re: [R] R CMD check errors
Thomas == Thomas Stabla [EMAIL PROTECTED]
on Wed, 10 Mar 2004 17:15:50 +0100 (CET) writes:
Thomas Hello,
Thomas I'm getting some error messages from R CMD check I can't deal with.
Thomas I'm working under Linux with R 1.8.1
Thomas The package working directory can be found at:
Thomas http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/distr.tar.gz
Thomas Here's the 00check.log produced by R CMD check distr
I got it and I can confirm to get warnings / errors along these
lines, also with today's R-1.9.0 alpha
Thomas * using log directory '/home/tom/studium/R/swp/swp/package/distr.Rcheck'
Thomas * checking for file 'distr/DESCRIPTION' ... OK
Thomas * checking if this is a source package ... OK
Thomas * checking package directory ... OK
Thomas * checking for portable file names ... OK
Thomas * checking for sufficient/correct file permissions ... OK
Thomas * checking DESCRIPTION meta-information ... OK
Thomas * checking index information ... OK
Thomas * checking package subdirectories ... WARNING
Thomas Subdirectory 'data' contains no data sets.
Thomas Subdirectory 'src' contains no source files.
(so just delete these two directories for now; but that doesn't
help for the real problem below !)
Thomas * checking R files for syntax errors ... OK
Thomas * checking R files for library.dynam ... OK
Thomas * checking S3 generic/method consistency ... WARNING
Thomas Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
Thomas package/namespace load failed
Thomas Execution halted
Thomas * checking for replacement functions with final arg not named 'value' ...
WARNING
Thomas Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
Thomas package/namespace load failed
Thomas Execution halted
Thomas * checking Rd files ... OK
Thomas * checking for missing documentation entries ... ERROR
Thomas Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc,
character.only = TRUE, verbose = FALSE) :
Yes, unfortunately, you don't get better errors here.
[[ - feature request ;-) ]]
But since R CMD check *does* install the package , you just
load/attach it manually
(using 'lib.loc = ... !) and can see what the matter is :
library(distr, lib.loc=/u/maechler/R/other-people/distr.Rcheck)
Error in loadNamespace(i[[1]], c(lib.loc, .libPaths()), keep.source) :
package 'stepfun' does not have a name space
Error in library(distr, lib.loc = /u/maechler/R/other-people/distr.Rcheck) :
package/namespace load failed
Now this does help you further.
Particularly for the above case, I'd recommend to
** Get and install R-1.9.0 alpha and exclusively work with R-1.9.x
** for the distr package.
Reason: From 1.9.0 on, stepfun is part of stats
- which *is* a namespace
- and a default package, i.e. you don't even have to
say library(stats) by default.
With high regards to the distr developers,
Martin
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Re: [R] R CMD check errors
Thomas Stabla wrote:
Hello,
I'm getting some error messages from R CMD check I can't deal with.
I'm working under Linux with R 1.8.1
The package working directory can be found at:
http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/distr.tar.gz
Here's the 00check.log produced by R CMD check distr
* using log directory '/home/tom/studium/R/swp/swp/package/distr.Rcheck'
* checking for file 'distr/DESCRIPTION' ... OK
* 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 index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'data' contains no data sets.
Subdirectory 'src' contains no source files.
So, if you don't want to provide data files or C/C++/Fortran sources,
you want to delete those directories.
BTW: There's no documentation in that package ...
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, character.only =
TRUE, verbose = FALSE) :
package/namespace load failed
Your NAMESPACE file is syntactically incorrect (hint: you need to quote
in exportPattern()). Please read Writing R extensions, and please read
the ReadMe files in all directories which have been created by
package.skeleton().
Uwe Ligges
Execution halted
* checking for replacement functions with final arg not named 'value' ... WARNING
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, character.only =
TRUE, verbose = FALSE) :
package/namespace load failed
Execution halted
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error in .tryQuietly({ : Error in library(package, lib.loc = lib.loc, character.only =
TRUE, verbose = FALSE) :
Thanks for your help,
Thomas Stabla
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RE: [R] R CMD check problems
In the directory where you ran the check, you should have a subdirectory like pkg.Rcheck (substitute pkg with the name of your package). That's where the package got installed for the purpose of the check. You could try to source() the files there and see if you can find the problem. HTH, Andy From: Joerg Schaber [mailto:[EMAIL PROTECTED] Hi, I am trying to create a R-package. When I load my R source files using source() for debugging reasons everthing works fine and all function also do want they are supposed to do. However, when I run 'R CMD check' it stop with * checking R files for syntax errors ... ERROR Syntax error in file Is there a way to further investigate where the error is? greetings, joerg __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R CMD check
The error was simply a missing end-of-line character in the last line in one of the R files. Thanks to Brian Ripley and Roger Bivand. -- John Bjornar Bremnes Norwegian Meteorological Institute (met.no) Research and Development Department P.O.Box 43 Blindern, N-0313 Oslo, Norway Phone: (+47) 2296 3326. Fax: (+47) 2269 6355 Prof Brian Ripley wrote: You have an error in the R files of your package. Before you even do R CMD check, do try loading the package in R. On Mon, 30 Jun 2003, John Bjørnar Bremnes wrote: when using R CMD check mypkg I get the error message ... * checking R files for library.dynam ... OK * checking generic/method consistency ... WARNING Error in .loadPackageQuietly(package, lib.loc) : Error in parse(file, n, text, prompt) : syntax error on line 95 Execution halted * checking for assignment functions with final arg not named 'value' ... WARNING Error in .loadPackageQuietly(package, lib.loc) : Error in parse(file, n, text, prompt) : syntax error on line 95 Execution halted ... What can I do to avoid this? I use R-1.7.0 on Linux RedHat. Any suggestions are appreciated. -- John Bjornar Bremnes Norwegian Meteorological Institute (met.no) Research and Development Department P.O.Box 43 Blindern, N-0313 Oslo, Norway Phone: (+47) 2296 3326. Fax: (+47) 2269 6355 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R CMD check
You have an error in the R files of your package. Before you even do R CMD check, do try loading the package in R. On Mon, 30 Jun 2003, John Bjørnar Bremnes wrote: when using R CMD check mypkg I get the error message ... * checking R files for library.dynam ... OK * checking generic/method consistency ... WARNING Error in .loadPackageQuietly(package, lib.loc) : Error in parse(file, n, text, prompt) : syntax error on line 95 Execution halted * checking for assignment functions with final arg not named 'value' ... WARNING Error in .loadPackageQuietly(package, lib.loc) : Error in parse(file, n, text, prompt) : syntax error on line 95 Execution halted ... What can I do to avoid this? I use R-1.7.0 on Linux RedHat. Any suggestions are appreciated. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R CMD check .
On Thu, 13 Feb 2003, Robin Hankin wrote: Hello everybody I'm writing a package and am trying to get it past R CMD check . It has no C or Fortan code, just R code. R CMD check . reports that the examples don't work: r:Davies% R CMD check . * checking for working latex ... OK * using log directory '/home/rksh/information/Davies/Davies.Rcheck' [deleted] * checking for code/documentation mismatches ... OK * checking for undocumented arguments in \usage ... OK * checking for CRLF line endings in C sources/headers ... OK * creating Davies-Ex.R ... OK * checking examples ... ERROR Running examples failed. r:Davies% Everything works fine with R CMD check --no-example . How do I tell which .Rd file is the problem? (I suspect that the examples aren't actually being executed because most of them take a long time and the error is pretty much instantaneous). Rcmd check makes a directory called libname.Rcheck. Inside that you will find a .Rout file which gives a log of the examples. If I understand the pattern it is called libname-Ed.Rout. Look at that file to see where the running of your examples failed. David Scott _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 AucklandNEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Webmaster, New Zealand Statistical Association: http://www.stat.auckland.ac.nz/nzsa/ __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R CMD check .
* checking for CRLF line endings in C sources/headers ... OK * creating Davies-Ex.R ... OK * checking examples ... ERROR Running examples failed. r:Davies% How do I tell which .Rd file is the problem? (I suspect that the examples aren't actually being executed because most of them take a long time and the error is pretty much instantaneous). You should have a directory named pkgName.Rcheck, inside of that there should be a file pkgname-Ex.Rout that should give you a clue as to what is happening (it is the R output from the examples running). -Jeff __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R CMD check .
Sorry, there was a typo in my answer: On Thu, 13 Feb 2003, David Scott wrote: . . . lots of stuff cut . . examples aren't actually being executed because most of them take a long time and the error is pretty much instantaneous). Rcmd check makes a directory called libname.Rcheck. Inside that you will find a .Rout file which gives a log of the examples. If I understand the pattern it is called libname-Ed.Rout. ^ Make that libname-Ex.Rout David Scott _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 AucklandNEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Webmaster, New Zealand Statistical Association: http://www.stat.auckland.ac.nz/nzsa/ __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R CMD check .
Hello everybody
thanks for your help with my R CMD check problem. The file
Davies-Ex.Rout does indeed contain a transcript of the examples.
I've found the .Rd file that contains the problem. The relevant
command executes perfectly when I cut-and-paste it onto the R command
line, but not when executed by R CMD check. How can this be?
[tail of Davies-Ex.Rout included below]
The first four lines work fine (including a function listing) but the
final line least.squares(rdavies(100,params)) fails, apparently
because the is.sorted argument doesn't take its default value of
FALSE. Anyone got any ideas as to why not?
robin
r:Davies.Rcheck% tail -27 Davies-Ex.Rout
##___ Examples ___:
params - c(10,0.1,-0.1)
rdavies(n=5,params)
[1] 10.367054 9.068977 9.409128 8.326713 9.885775
ddavies(10,params)
[1] 0.25
least.squares
function (data, print = FALSE, is.sorted = FALSE, start.v = NULL)
{
if (is.sorted == FALSE) {
data - sort(data)
}
if (is.null(start.v)) {
start.v - start.davies(data)
}
jj - optim(start.v, objective, dataset = data, is.sorted = TRUE)
if (print != TRUE) {
return(jj$par)
}
else {
return(list(parameters = jj$par, error = jj$value))
}
}
least.squares(rdavies(100,params))
Error in if (is.sorted == FALSE) { : missing value where logical needed
Execution halted
r:Davies.Rcheck%
--
Robin Hankin, Lecturer,
School of Geography and Environmental Science
Tamaki Campus
Private Bag 92019 Auckland
New Zealand
[EMAIL PROTECTED]
tel 0064-9-373-7599 x6820; FAX 0064-9-373-7042
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