[Rcpp-devel] Installation Problem
Sean Robert McGuffee
sean.mcguffee at gmail.com
Wed Mar 23 05:20:06 CET 2011
Hi,
I’m new to using C++ inside of R. I got a test program to work, so
it’s time for me to attach some function to it. I seem to be having
some issues though. I wonder if anyone out there can help me
understand the results I am getting. I’ve got to a point where it
seems to me that everything is installing but then afterwards it
segmentation faults. In particular the following are the parts where
the problem comes up:
** testing if installed package can be loaded
*** caught segfault ***
address 0x20, cause 'memory not mapped'
If anyone has any suggestions, please let me know. The full version of
the installation command and results is below:
Thanks,
Sean
Results:
install.packages("/Users/smcguffee/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS_HOME/R_PACKAGES/alignR_1.0.tar.gz",repos=NULL,type="source",INSTALL_opts="--no-multiarch")
Installing package(s) into ‘/Users/smcguffee/Library/R/2.12/library’
(as ‘lib’ is unspecified)
Attaching package: 'utils'
The following object(s) are masked from 'package:Rcpp':
.DollarNames, prompt
The following object(s) are masked from 'package:inline':
package.skeleton
* installing *source* package ‘alignR’ ...
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS/LIBSRM/INC/
-I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
-fPIC -g -O2 -c CAlias.cpp -o CAlias.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS/LIBSRM/INC/
-I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
-fPIC -g -O2 -c CBedFileLine.cpp -o CBedFileLine.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS/LIBSRM/INC/
-I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
-fPIC -g -O2 -c CBiologicalSymbol.cpp -o CBiologicalSymbol.o
.
. (trimmed because the group has a ridiculous size limit)
.
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS/LIBSRM/INC/
-I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
-fPIC -g -O2 -c char_traits_specialized_for_srm.cpp -o
char_traits_specialized_for_srm.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS/LIBSRM/INC/
-I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
-fPIC -g -O2 -c colorSpaceToSequenceSpace.cpp -o
colorSpaceToSequenceSpace.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS/LIBSRM/INC/
-I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
-fPIC -g -O2 -c genomeDataBase.cpp -o genomeDataBase.o
Attaching package: 'utils'
The following object(s) are masked from 'package:Rcpp':
.DollarNames, prompt
The following object(s) are masked from 'package:inline':
package.skeleton
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o alignR.so CAlias.o CBedFileLine.o
CBiologicalSymbol.o CClusterData.o CComparisonFunctions.o
CFourLetterChar.o CIndexedSequenceSet.o CLengthMappedSequenceSet.o
CMappedSequence.o CMappedSequenceSet.o CNucleicAcidChar.o CSRM.o
CSRMAlignment.o CSRMArgs.o CSRMColorSpace.o CSRMCurveFit.o
CSRMDNAFeatures.o CSRMFasta.o CSRMFileStuff.o CSRMGenomeDataBase.o
CSRMMath.o CSRMOverlapStats.o CSRMPDB.o CSRMSharkDataSource.o
CSRMSharkFFNet.o CSRMString.o CSRMTabbedData.o CSRMThread.o
CSequence.o CSequenceSet.o CSequenceSetLocation.o CStringDNA.o CTab.o
CTabData.o CTabDataSet.o C_Atom.o C_BED.o
C_CategoriesOfExpressionData.o C_Correlation.o C_GFF.o C_GO.o
C_Histogram.o C_MIX_BED_AND_SGD.o C_Mechanics.o
C_Mix_Comparison_And_Cluster.o C_Mix_Comparison_And_Fasta.o
C_Mix_Comparison_And_Sgr.o C_Mix_GFF_And_SGD.o
C_Mix_GFF_And_Transcript.o C_Mix_GFF_And_TypeOfTranscript.o
C_Mix_GenomeDataBase_And_SGR.o C_Mix_SGR_FASTA.o
C_Mix_Transcript_And_TranscriptGroup.o C_MultiHistogram.o
C_PeriodicTable.o C_RandomNumberGenerator.o C_SGD.o C_SGR.o
C_SGR_Chromosome.o C_SequenceStats.o C_SizeRange.o C_Superimpose.o
C_Transcript.o C_TranscriptGroup.o C_TypeOfAtom.o C_TypeOfTranscript.o
C_XYZ.o CssFASTA.o Sequence.o SequenceSet.o SgrFile.o
char_traits_specialized_for_srm.o colorSpaceToSequenceSpace.o
genomeDataBase.o
/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/lib/x86_64/libRcpp.a
/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS/LIBSRM/LIB/libsrm.SeanBenchGcc.so
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
Attaching package: 'utils'
The following object(s) are masked from 'package:Rcpp':
.DollarNames, prompt
The following object(s) are masked from 'package:inline':
package.skeleton
installing to /Users/smcguffee/Library/R/2.12/library/alignR/libs/x86_64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
*** caught segfault ***
address 0x20, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e)
if (!is.null(call)) { if (identical(call[[1L]],
quote(doTryCatch))) call <- sys.call(-4L) dcall <-
deparse(call)[1L] prefix <- paste("Error in", dcall, ": ")
LONG <- 75L msg <- conditionMessage(e) sm <-
strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") +
nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L +
nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
if (w > LONG) prefix <- paste(prefix, "\n ", sep =
"") } else prefix <- "Error : " msg <- paste(prefix,
conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error"))})
8: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc),
keep.source = keep.source) dataPath <- file.path(which.lib.loc,
package, "data") env <- attachNamespace(ns, pos = pos, dataPath =
dataPath, deps)})
9: library(pkg_name, lib.loc = lib, character.only = TRUE,
logical.return = TRUE)
10: withCallingHandlers(expr, packageStartupMessage = function(c)
invokeRestart("muffleMessage"))
11: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE))
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) { call <- conditionCall(e)
if (!is.null(call)) { if (identical(call[[1L]],
quote(doTryCatch))) call <- sys.call(-4L) dcall <-
deparse(call)[1L] prefix <- paste("Error in", dcall, ": ")
LONG <- 75L msg <- conditionMessage(e) sm <-
strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") +
nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L +
nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
if (w > LONG) prefix <- paste(prefix, "\n ", sep =
"") } else prefix <- "Error : " msg <- paste(prefix,
conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error"))})
16: try(suppressPackageStartupMessages(library(pkg_name, lib.loc =
lib, character.only = TRUE, logical.return = TRUE)))
17: do_install_source(pkg_name, instdir, pkg, desc)
18: do_install(pkg)
19: tools:::.install_packages()
aborting ...
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 24298
Done echo 'tools:::.install_packages()'
24299 Segmentation fault | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" $myArgs --slave --args ${args}
Warning message:
In install.packages("/Users/smcguffee/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS_HOME/R_PACKAGES/alignR_1.0.tar.gz",
:
installation of package
'/Users/smcguffee/WHITEHOUSE_LAB/WHITEHOUSE_LAB_PROGRAMS_HOME/R_PACKAGES/alignR_1.0.tar.gz'
had non-zero exit status
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