Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "new", "new" : duplicate 'row.names' are not allowed Calls: <Anonymous> ... rownames<- -> row.names<- -> row.names<-.data.frame Execution halted ----------------- yet everything is okey dokey at http://bioconductor.org/checkResults/2.7/bioc-LATEST/#S under the snpMatrix entry. I believe it might be a bug in codetools::incLocalSrcInfo (used by "R CMD check") and here is what I think the fix(?) - but I am not entirely sure what that routine does and why other package writers haven't noticed similiar problems before: diff -ur codetools/R/codetools.R codetools-fix/R/codetools.R --- codetools/R/codetools.R 2011-01-07 15:52:58.000000000 +0000 +++ codetools-fix/R/codetools.R 2011-02-03 10:03:54.000000000 +0000 @@ -823,8 +823,9 @@ new <- list(srcfile = if (is.null(w$srcfile)) NA_character_ else w$srcfile, frow = if (is.null(w$frow)) NA_integer_ else w$frow, lrow = if (is.null(w$lrow)) NA_integer_ else w$lrow) + new <- as.data.frame(new, stringsAsFactors = FALSE) if (is.null(value)) - value <- as.data.frame(new, stringsAsFactors = FALSE) + value <- new else value <- rbind(value, new) assign("srcinfo", value, entry) Apply this "fix" would result in snpMatrix's "R CMD check" churning out: --------------------- .ld.withmany: local variable ?names.components? assigned but may not be used .ld.withmany: local variable ?nsnps.for.each? assigned but may not be used misinherits: local variable ?nc.snps? assigned but may not be used misinherits: local variable ?nr.snps? assigned but may not be used qq.chisq: local variable ?lab? assigned but may not be used read.HapMap.data: local variable ?base? assigned but may not be used read.HapMap.data: local variable ?build? assigned but may not be used read.HapMap.data: local variable ?finish? assigned but may not be used read.HapMap.data: local variable ?strand? assigned but may not be used tdt.snp: local variable ?nc.snps? assigned but may not be used tdt.snp: local variable ?nr.snps? assigned but may not be used --------------------- which is more like expected check warnings. Care to comment? Hin-Tak Leung
bug in codetools/R CMD check?
5 messages · Luke Tierney, Hin-Tak Leung, Brian Ripley
5 days later
Thanks -- will try to have a look sometime soon. luke
On Thu, 3 Feb 2011, Hin-Tak Leung wrote:
Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "new", "new" : duplicate 'row.names' are not allowed Calls: <Anonymous> ... rownames<- -> row.names<- -> row.names<-.data.frame Execution halted ----------------- yet everything is okey dokey at http://bioconductor.org/checkResults/2.7/bioc-LATEST/#S under the snpMatrix entry. I believe it might be a bug in codetools::incLocalSrcInfo (used by "R CMD check") and here is what I think the fix(?) - but I am not entirely sure what that routine does and why other package writers haven't noticed similiar problems before: diff -ur codetools/R/codetools.R codetools-fix/R/codetools.R --- codetools/R/codetools.R 2011-01-07 15:52:58.000000000 +0000 +++ codetools-fix/R/codetools.R 2011-02-03 10:03:54.000000000 +0000 @@ -823,8 +823,9 @@ new <- list(srcfile = if (is.null(w$srcfile)) NA_character_ else w$srcfile, frow = if (is.null(w$frow)) NA_integer_ else w$frow, lrow = if (is.null(w$lrow)) NA_integer_ else w$lrow) + new <- as.data.frame(new, stringsAsFactors = FALSE) if (is.null(value)) - value <- as.data.frame(new, stringsAsFactors = FALSE) + value <- new else value <- rbind(value, new) assign("srcinfo", value, entry) Apply this "fix" would result in snpMatrix's "R CMD check" churning out: --------------------- .ld.withmany: local variable ?names.components? assigned but may not be used .ld.withmany: local variable ?nsnps.for.each? assigned but may not be used misinherits: local variable ?nc.snps? assigned but may not be used misinherits: local variable ?nr.snps? assigned but may not be used qq.chisq: local variable ?lab? assigned but may not be used read.HapMap.data: local variable ?base? assigned but may not be used read.HapMap.data: local variable ?build? assigned but may not be used read.HapMap.data: local variable ?finish? assigned but may not be used read.HapMap.data: local variable ?strand? assigned but may not be used tdt.snp: local variable ?nc.snps? assigned but may not be used tdt.snp: local variable ?nr.snps? assigned but may not be used --------------------- which is more like expected check warnings. Care to comment? Hin-Tak Leung
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Luke Tierney
Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke at stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
--- On Tue, 8/2/11, luke-tierney at uiowa.edu <luke-tierney at uiowa.edu> wrote:
From: luke-tierney at uiowa.edu <luke-tierney at uiowa.edu> Subject: Re: [Rd] bug in codetools/R CMD check? To: "Hin-Tak Leung" <htl10 at users.sourceforge.net> Cc: david.clayton at cimr.cam.ac.uk, r-devel at r-project.org Date: Tuesday, 8 February, 2011, 15:34 Thanks -- will try to have a look sometime soon. luke
Thanks. Also, regardless of whether that's a bug in codetools or snpMatrix (I am okay if you turn this around to say there is some coding style we shouldn't do in there, for which I'd apologize), there seems to be a small bug or inconsistency, and certainly in R or codetools, in that the codetools message is shown in all 4 platforms - linux, mac, win32, win64 - but the error status, whether it is correct or not, only propagate back up to the "R CMD check" harness in the case of win64 and not for the other 3 platforms. It should pass or fail with a warning consistently on all platforms. Hin-Tak
On Thu, 3 Feb 2011, Hin-Tak Leung wrote:
Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD
check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+)
e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names':
?new?
Error in `row.names<-.data.frame`(`*tmp*`, value =
c("1", "new", "new" :
? duplicate 'row.names' are not allowed Calls: <Anonymous> ... rownames<- ->
row.names<- -> row.names<-.data.frame
Execution halted ----------------- yet everything is okey dokey at http://bioconductor.org/checkResults/2.7/bioc-LATEST/#S
under the snpMatrix entry.
I believe it might be a bug in
codetools::incLocalSrcInfo (used by "R CMD check") and here is what I think the fix(?) - but I am not entirely sure what that routine does and why other package writers haven't noticed similiar problems before:
diff -ur codetools/R/codetools.R
codetools-fix/R/codetools.R
--- codetools/R/codetools.R???
2011-01-07 15:52:58.000000000 +0000
+++ codetools-fix/R/codetools.R???
2011-02-03 10:03:54.000000000 +0000
@@ -823,8 +823,9 @@ ? ???new <- list(srcfile = if
(is.null(w$srcfile)) NA_character_ else w$srcfile,
? ? ? ? ? ? ?
???frow = if (is.null(w$frow)) NA_integer_ else w$frow,
? ? ? ? ? ? ?
???lrow = if (is.null(w$lrow)) NA_integer_ else w$lrow)
+? ? new <- as.data.frame(new,
stringsAsFactors = FALSE)
? ???if (is.null(value)) -? ? ? ? value <-
as.data.frame(new, stringsAsFactors = FALSE)
+? ? ? ? value <- new ? ???else ? ? ? ???value <-
rbind(value, new)
? ???assign("srcinfo", value,
entry)
Apply this "fix" would result in snpMatrix's "R CMD
check" churning out:
--------------------- .ld.withmany: local variable ?names.components?
assigned but may not be used
.ld.withmany: local variable ?nsnps.for.each?
assigned but may not be used
misinherits: local variable ?nc.snps? assigned but
may not be used
misinherits: local variable ?nr.snps? assigned but
may not be used
qq.chisq: local variable ?lab? assigned but may
not be used
read.HapMap.data: local variable ?base? assigned
but may not be used
read.HapMap.data: local variable ?build? assigned
but may not be used
read.HapMap.data: local variable ?finish? assigned
but may not be used
read.HapMap.data: local variable ?strand? assigned
but may not be used
tdt.snp: local variable ?nc.snps? assigned but may
not be used
tdt.snp: local variable ?nr.snps? assigned but may
not be used
--------------------- which is more like expected check warnings. Care to comment? Hin-Tak Leung
______________________________________________ R-devel at r-project.org
mailing list
-- Luke Tierney Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa? ? ? ? ? ? ? ? ? Phone:? ? ? ? ? ???319-335-3386 Department of Statistics and? ? ? ? Fax:? ? ? ? ? ? ???319-335-3017 ? ? Actuarial Science 241 Schaeffer Hall? ? ? ? ? ? ? ? ? email:? ? ? luke at stat.uiowa.edu Iowa City, IA 52242? ? ? ? ? ? ? ???WWW:? http://www.stat.uiowa.edu
On Tue, 8 Feb 2011, Hin-Tak Leung wrote:
--- On Tue, 8/2/11, luke-tierney at uiowa.edu <luke-tierney at uiowa.edu> wrote:
From: luke-tierney at uiowa.edu <luke-tierney at uiowa.edu> Subject: Re: [Rd] bug in codetools/R CMD check? To: "Hin-Tak Leung" <htl10 at users.sourceforge.net> Cc: david.clayton at cimr.cam.ac.uk, r-devel at r-project.org Date: Tuesday, 8 February, 2011, 15:34 Thanks -- will try to have a look sometime soon. luke
Thanks. Also, regardless of whether that's a bug in codetools or snpMatrix (I am okay if you turn this around to say there is some coding style we shouldn't do in there, for which I'd apologize), there seems to be a small bug or inconsistency, and certainly in R or codetools, in that the codetools message is shown in all 4 platforms - linux, mac, win32, win64 - but the error status, whether it is correct or not, only propagate back up to the "R CMD check" harness in the case of win64 and not for the other 3 platforms. It should pass or fail with a warning consistently on all platforms.
Are you sure this is the same version of R and codetools? If you mean BioC's check farm, that often has version skew. I see the message consistently on all my platforms ....
Hin-Tak
On Thu, 3 Feb 2011, Hin-Tak Leung wrote:
Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD
check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+)
e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names':
?new?
Error in `row.names<-.data.frame`(`*tmp*`, value =
c("1", "new", "new" :
? duplicate 'row.names' are not allowed Calls: <Anonymous> ... rownames<- ->
row.names<- -> row.names<-.data.frame
Execution halted ----------------- yet everything is okey dokey at http://bioconductor.org/checkResults/2.7/bioc-LATEST/#S
under the snpMatrix entry.
I believe it might be a bug in
codetools::incLocalSrcInfo (used by "R CMD check") and here is what I think the fix(?) - but I am not entirely sure what that routine does and why other package writers haven't noticed similiar problems before:
diff -ur codetools/R/codetools.R
codetools-fix/R/codetools.R
--- codetools/R/codetools.R???
2011-01-07 15:52:58.000000000 +0000
+++ codetools-fix/R/codetools.R???
2011-02-03 10:03:54.000000000 +0000
@@ -823,8 +823,9 @@ ? ???new <- list(srcfile = if
(is.null(w$srcfile)) NA_character_ else w$srcfile,
? ? ? ? ? ? ?
???frow = if (is.null(w$frow)) NA_integer_ else w$frow,
? ? ? ? ? ? ?
???lrow = if (is.null(w$lrow)) NA_integer_ else w$lrow)
+? ? new <- as.data.frame(new,
stringsAsFactors = FALSE)
? ???if (is.null(value)) -? ? ? ? value <-
as.data.frame(new, stringsAsFactors = FALSE)
+? ? ? ? value <- new ? ???else ? ? ? ???value <-
rbind(value, new)
? ???assign("srcinfo", value,
entry)
Apply this "fix" would result in snpMatrix's "R CMD
check" churning out:
--------------------- .ld.withmany: local variable ?names.components?
assigned but may not be used
.ld.withmany: local variable ?nsnps.for.each?
assigned but may not be used
misinherits: local variable ?nc.snps? assigned but
may not be used
misinherits: local variable ?nr.snps? assigned but
may not be used
qq.chisq: local variable ?lab? assigned but may
not be used
read.HapMap.data: local variable ?base? assigned
but may not be used
read.HapMap.data: local variable ?build? assigned
but may not be used
read.HapMap.data: local variable ?finish? assigned
but may not be used
read.HapMap.data: local variable ?strand? assigned
but may not be used
tdt.snp: local variable ?nc.snps? assigned but may
not be used
tdt.snp: local variable ?nr.snps? assigned but may
not be used
--------------------- which is more like expected check warnings. Care to comment? Hin-Tak Leung
______________________________________________ R-devel at r-project.org
mailing list
-- Luke Tierney Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa? ? ? ? ? ? ? ? ? Phone:? ? ? ? ? ???319-335-3386 Department of Statistics and? ? ? ? Fax:? ? ? ? ? ? ???319-335-3017 ? ? Actuarial Science 241 Schaeffer Hall? ? ? ? ? ? ? ? ? email:? ? ? luke at stat.uiowa.edu Iowa City, IA 52242? ? ? ? ? ? ? ???WWW:? http://www.stat.uiowa.edu
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Brian D. Ripley, ripley at stats.ox.ac.uk 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, UK Fax: +44 1865 272595
--- On Tue, 8/2/11, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
From: Prof Brian Ripley <ripley at stats.ox.ac.uk> Subject: Re: [Rd] bug in codetools/R CMD check? To: "Hin-Tak Leung" <htl10 at users.sourceforge.net> Cc: luke-tierney at uiowa.edu, david.clayton at cimr.cam.ac.uk, r-devel at r-project.org Date: Tuesday, 8 February, 2011, 17:36 On Tue, 8 Feb 2011, Hin-Tak Leung wrote:
--- On Tue, 8/2/11, luke-tierney at uiowa.edu
<luke-tierney at uiowa.edu> wrote:
From: luke-tierney at uiowa.edu
<luke-tierney at uiowa.edu>
Subject: Re: [Rd] bug in codetools/R CMD check? To: "Hin-Tak Leung" <htl10 at users.sourceforge.net> Cc: david.clayton at cimr.cam.ac.uk,
r-devel at r-project.org
Date: Tuesday, 8 February, 2011, 15:34 Thanks -- will try to have a look sometime soon. luke
Thanks. Also, regardless of whether that's a bug in codetools
or snpMatrix
(I am okay if you turn this around to say there is
some coding style
we shouldn't do in there, for which I'd apologize),
there seems to
be a small bug or inconsistency, and certainly in R or
codetools, in
that the codetools message is shown in all 4 platforms
- linux, mac,
win32, win64 - but the error status, whether it is
correct or not,
only propagate back up to the "R CMD check" harness in
the case of
win64 and not for the other 3 platforms. It should
pass or fail with
a warning consistently on all platforms.
Are you sure this is the same version of R and codetools?? If you mean BioC's check farm, that often has version skew.? I see the message consistently on all my platforms ....
That's what I mean - the codetools message are seen consistently on all platforms, but the warning status only propagate back up to R CMD check (and resulted in a "1 warning" status) for win64 only; so R CMD check is behaving inconsistently, regardless of whether the message is genuine or not. http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/gewurz-checksrc.html * using R version 2.12.1 (2010-12-16) * using platform: x86_64-pc-mingw32 (64-bit) codetools message, status 1, 1 warning http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/pelham-checksrc.html * using R version 2.12.1 Patched (2010-12-17 r53867) * using platform: i386-apple-darwin9.8.0 (32-bit) codetools message, no error status, no warning http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/liverpool-checksrc.html * using R version 2.12.1 (2010-12-16) * using platform: i386-pc-mingw32 (32-bit) codetools message, status 1, no warning http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html * using R version 2.12.1 (2010-12-16) * using platform: x86_64-unknown-linux-gnu (64-bit) codetools message, no error status, no warning The mac OS X box has a slightly different version of R, but the other seems to be the same, and yet the error status and also whether the warning status is propate back is different. The codetools message is seen in all cases. Hin-Tak