MichaelChirico
commented
4 years ago From: ripley@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::> On Tue, 13 Aug 2002 hb@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::> wrote:
Full_Name: Henrik Bengtsson
Version: 1.5.1
OS: WinMe
Submission from: (NULL) (217.210.0.243)
In the Perl script $R_HOME/bin/check there is a bug under the section "Check
R
code for syntax errors" where the 'Rfiles <- c(...)' is build up. If there
are
too many files in @Rfiles the source code line generated will be too long and
weird things will happen, e.g. strange bytes/characters will be inserted.SUGGESTION/SOLUTION:
Add a new line character after each "join";
$Rcmd .= join("\",\n \"", @Rfiles) . "\")\n";
instead of
$Rcmd .= join("\", \"", @Rfiles) . "\")\n";
SUGGESTION II:
I ran into similar problems in other situations where I autogenerated too
long
source lines. The errors where hard to reproduce and took time to find. It
would
be nice if the [R] parser, or some previous engine that reads the source
file,
could given an explicit error saying that the "line was too long".
EXAMPLE:
In my case I got in perl '@Rfiles' was:
"R/LogBook.R R/LogEntry.R R/GenePixData.R R/Layout.R R/ImaGeneData.R
R/MicroarrayData.PLOT.R R/QualityData.R R/MicroarrayData.R R/MAData.R
R/MAData.NORM.R R/zzz.R R/Replicates.R R/SMA.R R/FieldFilter.R R/Filter.R
R/QuantArrayData.R R/RGData.R R/RawData.R R/000.R R/MicroarrayData.IO.R
R/LayoutGroups.R R/BFilter.R R/com.braju.sma.R R/Copy of TFilter.R R/Copy of
SSMatrix.R R/private.utils.R R/WangetalData.R R/KHessFilter.R R/DfFilter.R
R/SpotData.R R/ScanAlyzeData.R R/BMAData.R R/AFilter.R R/MFilter.R
R/Layout.obsolete.R R/AndFilter.R R/OrFilter.R R/SEFilter.R R/TFilter.R
R/AcceptFilter.R R/SpotPosition.R R/SerialFilter.R R/GSRArray.R
R/MultiwayArray.R R/KHessData.R R/GeneAcceptFilter.R R/GeneData.R
R/GeneRejectFilter.R R/TMAData.R R/NotFilter.R R/ParallelFilter.R
R/RejectFilter.R R/ReplicateOutlierFilter.R R/WorkData.R R/Matrix.R
R/MicroarrayData.LOG.R R/MicroarrayData.NORM.R R/SSMatrix.R"
but in [R] 'Rfiles' became:
[1] "R/LogBook.R" "R/LogEntry.R"
[3] "R/GenePixData.R" "R/Layout.R"
[5] "R/ImaGeneData.R" "R/MicroarrayData.PLOT.R"
[7] "R/QualityData.R" "R/MicroarrayData.R"
[9] "R/MAData.R" "R/MAData.NORM.R"
[11] "R/zzz.R" "R/Replicates.R"
[13] "R/SMA.R" "R/FieldFilter.R"
[15] "R/Filter.R" "R/QuantArrayData.R"
[17] "R/RGData.R" "R/RawData.R"
[19] "R/000.R" "R/MicroarrayData.IO.R"
[21] "R/LayoutGroups.R" "R/BFilter.R"
[23] "R/com.braju.sma.R" "R/Copy of TFilter.R"
[25] "R/Copy of SSMatrix.R" "R/private.utils.R"
[27] "R/WangetalData.R" "R/KHessFilter.R"
[29] "R/DfFilter.R" "R/SpotData.R"
[31] "R/ScanAlyzeData.R" "R/BMAData.R"
[33] "R/AFilter.R" "R/MFilter.R"
[35] "R/Layout.obsolete.R" "R/AndFilter.R"
[37] "R/OrFilter.R" "R/SEFilter.R"
[39] "R/TFilter.R" "R/AcceptFilter.R"
[41] "R/SpotPosition.R" "R/SerialFilter.R"
[43] "R/GSRArray.R" "R/MultiwayArray.R"
[45] "R/KHessData.R" "R/GeneAcceptFilter.R"
[47] "R/GeneData.R" "R/GeneRejectFilter.R"
[49] "R/TMAData.R" "R/NotFilter.R"
[51] "R/ParallelFilter.R" "R/RejectFilter.R"
[53] "R/ReplicateOutlierFilter.R" "R/WorkData.R"
[55] "R/Matrix.R" "R/Micr\b‘_ÜIoarrayData.LOG.R"
[57] "R/MicroarrayData.NORM.R" "R/SSMatrix.R"
Look at the 56 element. Trying to add or remove files, I found that this was
always happening at the same column in the Rfiles row and inferred that this
is
due to the maximum line length in [R] source files. Correct?There is no such line limit. If I take your file list, convert it via the orginal join and read it into R, I don't get a problem, under Linux or Windows XP. I think you are hitting the limitations of your `operating system', not R. But without a reproducible example it is hard to tell.
Package survival has 92 files with file names at least as long as yours, and that works perfectly happily on Windows XP.
Can you make available a sample package which exhibits the problem?
Nevertheless, joining with "\n" should be a palliative measure.
-- Brian D. Ripley, ripley@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ <CENSORING FROM DETECTED PHONE NUMBER ONWARDS; SEE BUGZILLA>
METADATA
- Comment author - Jitterbug compatibility account
- Timestamp - 2002-08-13 14:43:03 UTC
From: hb@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::> Full_Name: Henrik Bengtsson Version: 1.5.1 OS: WinMe Submission from: (NULL) (217.210.0.243)
In the Perl script $R_HOME/bin/check there is a bug under the section "Check R code for syntax errors" where the 'Rfiles <- c(...)' is build up. If there are too many files in @Rfiles the source code line generated will be too long and weird things will happen, e.g. strange bytes/characters will be inserted.
SUGGESTION/SOLUTION: Add a new line character after each "join";
$Rcmd .= join("\",\n \"", @Rfiles) . "\")\n";
instead of
$Rcmd .= join("\", \"", @Rfiles) . "\")\n";
SUGGESTION II: I ran into similar problems in other situations where I autogenerated too long source lines. The errors where hard to reproduce and took time to find. It would be nice if the [R] parser, or some previous engine that reads the source file, could given an explicit error saying that the "line was too long".
EXAMPLE: In my case I got in perl '@Rfiles' was: "R/LogBook.R R/LogEntry.R R/GenePixData.R R/Layout.R R/ImaGeneData.R R/MicroarrayData.PLOT.R R/QualityData.R R/MicroarrayData.R R/MAData.R R/MAData.NORM.R R/zzz.R R/Replicates.R R/SMA.R R/FieldFilter.R R/Filter.R R/QuantArrayData.R R/RGData.R R/RawData.R R/000.R R/MicroarrayData.IO.R R/LayoutGroups.R R/BFilter.R R/com.braju.sma.R R/Copy of TFilter.R R/Copy of SSMatrix.R R/private.utils.R R/WangetalData.R R/KHessFilter.R R/DfFilter.R R/SpotData.R R/ScanAlyzeData.R R/BMAData.R R/AFilter.R R/MFilter.R R/Layout.obsolete.R R/AndFilter.R R/OrFilter.R R/SEFilter.R R/TFilter.R R/AcceptFilter.R R/SpotPosition.R R/SerialFilter.R R/GSRArray.R R/MultiwayArray.R R/KHessData.R R/GeneAcceptFilter.R R/GeneData.R R/GeneRejectFilter.R R/TMAData.R R/NotFilter.R R/ParallelFilter.R R/RejectFilter.R R/ReplicateOutlierFilter.R R/WorkData.R R/Matrix.R R/MicroarrayData.LOG.R R/MicroarrayData.NORM.R R/SSMatrix.R"
but in [R] 'Rfiles' became: [1] "R/LogBook.R" "R/LogEntry.R"
[3] "R/GenePixData.R" "R/Layout.R"
[5] "R/ImaGeneData.R" "R/MicroarrayData.PLOT.R"
[7] "R/QualityData.R" "R/MicroarrayData.R"
[9] "R/MAData.R" "R/MAData.NORM.R"
[11] "R/zzz.R" "R/Replicates.R"
[13] "R/SMA.R" "R/FieldFilter.R"
[15] "R/Filter.R" "R/QuantArrayData.R"
[17] "R/RGData.R" "R/RawData.R"
[19] "R/000.R" "R/MicroarrayData.IO.R"
[21] "R/LayoutGroups.R" "R/BFilter.R"
[23] "R/com.braju.sma.R" "R/Copy of TFilter.R"
[25] "R/Copy of SSMatrix.R" "R/private.utils.R"
[27] "R/WangetalData.R" "R/KHessFilter.R"
[29] "R/DfFilter.R" "R/SpotData.R"
[31] "R/ScanAlyzeData.R" "R/BMAData.R"
[33] "R/AFilter.R" "R/MFilter.R"
[35] "R/Layout.obsolete.R" "R/AndFilter.R"
[37] "R/OrFilter.R" "R/SEFilter.R"
[39] "R/TFilter.R" "R/AcceptFilter.R"
[41] "R/SpotPosition.R" "R/SerialFilter.R"
[43] "R/GSRArray.R" "R/MultiwayArray.R"
[45] "R/KHessData.R" "R/GeneAcceptFilter.R"
[47] "R/GeneData.R" "R/GeneRejectFilter.R"
[49] "R/TMAData.R" "R/NotFilter.R"
[51] "R/ParallelFilter.R" "R/RejectFilter.R"
[53] "R/ReplicateOutlierFilter.R" "R/WorkData.R"
[55] "R/Matrix.R" "R/Micr\b‘_ÜIoarrayData.LOG.R" [57] "R/MicroarrayData.NORM.R" "R/SSMatrix.R"
Look at the 56 element. Trying to add or remove files, I found that this was always happening at the same column in the Rfiles row and inferred that this is due to the maximum line length in [R] source files. Correct?
Best wishes
Henrik Bengtsson
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