Hi,
We recently upgraded to a new remote linux box, so I took the opportunity to install R 2.15.0, and then my selected bioconductor packages, including xcms 1.32.0 via the biocLite() method. However, xcms failed to install, citing that mzR wasn't available. I at first thought this was because I forgot to re-install the netCDF library (the paths had changed to the new box), so I reinstalled netCDF and then tried xcms installation again - still fails. I'm not sure what to do next.
Of possible note: I have used the --prefix options to install R and netcdf to my user-defined locations; it's not possible to install either as root as I am using a networked shared box.
Some details:
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.4.4
loaded via a namespace (and not attached):
[1] tools_2.15.0
netCDF installation method:
netCDF installation (it all checks out on make check):
tar -zxvf netcdf-3.6.3.tar.gz
cd netcdf-3.6.3
./configure --prefix=/bdc/people/trl1/bin --enable-shared CFLAGS="-fPIC"
make
make install
failed xcms installation (also note that setting dependencies=F has no effect of preventing the mzR installation attempt):
> biocLite("xcms")
BioC_mirror: http://bioconductor.org (http://bioconductor.org)
Using R version 2.15, BiocInstaller version 1.4.4.
Installing package(s) 'xcms'
also installing the dependency ‘mzR’
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/mzR_1.2.1.tar.gz'
Content type 'application/x-gzip' length 4893749 bytes (4.7 Mb)
opened URL
==================================================
downloaded 4.7 Mb
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/xcms_1.32.0.tar.gz'
Content type 'application/x-gzip' length 1320111 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb
* installing *source* package ‘mzR’ ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/thread/src/pthread/once.o ./boost/filesystem/src/operations.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o
g++ -I/bdc/people/trl1/bin/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/bdc/people/trl1/bin/lib64/R/library/Rcpp/include" -fpic -g -O2 -c cramp.cpp -o cramp.o
g++ -I/bdc/people/trl1/bin/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/bdc/people/trl1/bin/lib64/R/library/Rcpp/include" -fpic -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -I/bdc/people/trl1/bin/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/bdc/people/trl1/bin/lib64/R/library/Rcpp/include" -fpic -g -O2 -c ramp.cpp -o ramp.o
g++ -I/bdc/people/trl1/bin/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/bdc/people/trl1/bin/lib64/R/library/Rcpp/include" -fpic -g -O2 -c RcppRamp.cpp -o RcppRamp.o
g++ -I/bdc/people/trl1/bin/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/bdc/people/trl1/bin/lib64/R/library/Rcpp/include" -fpic -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -std=gnu99 -I/bdc/people/trl1/bin/lib64/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -I/usr/local/include -I"/bdc/people/trl1/bin/lib64/R/library/Rcpp/include" -fpic -g -O2 -c rnetCDF.c -o rnetCDF.o
rnetCDF.c:2:20: fatal error: netcdf.h: No such file or directory
compilation terminated.
make: *** [rnetCDF.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/bdc/people/trl1/bin/lib64/R/library/mzR’
ERROR: dependency ‘mzR’ is not available for package ‘xcms’
* removing ‘/bdc/people/trl1/bin/lib64/R/library/xcms’
The downloaded source packages are in
‘/tmp/RtmpcsZOLu/downloaded_packages’
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘mzR’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘xcms’ had non-zero exit status
>
Hi,
in the case of custom locations for netcdf you will have to unpack the mzR sources
and edit mzR/src/Makevars to add your locations to
PKG_CPPFLAGS and PKG_LIBS.
Yours,
Steffen
OK - thought so.
I've managed a dirty workaround instead that works. Basically, I did 3 consecutive installs of netcdf, configured each time for my ~/usr directory, ~/usr/bin, and ~/usr/bin/lib64/R. Interestingly, the ncdf library in R loaded fine with just the ~/usr install, but mzR (and xcms) required additionally the other two locations to install properly.
This was all with the latest netCDF build (4.2) with the --disable-netcdf-4 option
cheers
Tony
This is probably not the same problem, but I very recently updated to R-2.15.0 and then tried to install xcms. My initial attempt failed due to the version of mzR that was downloaded using the installation procedure at http://metlin.scripps.edu/xcms/installation.php (http://metlin.scripps.edu/xcms/installation.php) failing to compile on my Linux 64-bit system with gcc-4.7. I manually downloaded the mzR_1.3.7.tar.gz source package from http://www.bioconductor.org/packages/2. ... 3.7.tar.gz (http://www.bioconductor.org/packages/2.11/bioc/src/contrib/mzR_1.3.7.tar.gz) and built the package from within R using install.package(c("/<path>/<to>/mzR_1.3.7.tar.gz")). With that in place, xcms was able to be successfully installed.
I just tried setting up my typical R environment on a new computer, i.e. R 2.15 and the current bioconductor-devel versions of XCMS and mzR. I installed with
source("http://bioconductor.org/biocLite.R")
biocLite("mzR")
useDevel()
biocLite("xcms")
The versions look right in the library; however, there seems to be a problem with mzR. When I attempt to load mzR, the first attempt fails with an error message. Note: this is true for both the 64- and 32-bit versions of R.
> library(mzR)
Loading required package: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
call: value[[3L]](cond)
error: failed to load module Ramp from package mzR
could not find function "errorOccured"
Error: package/namespace load failed for ‘mzR’
Interestingly, when I try the exact same thing again in the same session, R crashes:
> library(mzR)
Problemsignatur:
Problemereignisname: APPCRASH
Anwendungsname: Rgui.exe
Anwendungsversion: 2.151.59607.0
Anwendungszeitstempel: 4fe47a63
Fehlermodulname: mzR.dll
[...]
Now I tried to download it by hand and reinstall, but I get the same problem:
> install.packages("D:/mzR_1.3.7.zip")
Installiere Paket(e) nach ‘D:/R/win-library/2.15’
(da ‘lib’ nicht spezifiziert)
leite 'repos = NULL' aus dem Dateinamen ab
Paket ‘mzR’ erfolgreich ausgepackt und MD5 Summen abgeglichen
> library(mzR)
Lade nötiges Paket: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
call: value[[3L]](cond)
error: failed to load module Ramp from package mzR
konnte Funktion "errorOccured" nicht finden
Fehler: Laden von Paket/Namensraum für ‘mzR’ fehlgeschlagen
>
Right now I'm trying to build from source.
I can confirm this. A bug report was sent to the mzR developers.
Ralf
Building from source worked, btw.
Hi,
if the build from source worked, there must be something wrong
with the way the BioC build farm creates the package, right ?
Also, can I have the version(s) of Rcpp that work and don't work ?
Since there hasn't been a change in mzR since mid-may,
I suspect the problem somewhere else.
Can we put your build of mzR somewhere and place a link here ?
This would of course only be a stopgap measure until the BioC
builds have been fixed. Currently, their windows build seems
to be unavailable.
Yours,
Steffen
Hi Steffen,
you have mail.
My Rcpp version is 0.9.11.
The mzR version which didn't work is:
http://www.bioconductor.org/packages/2. ... _1.3.7.zip (http://www.bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/mzR_1.3.7.zip)
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252
[3] LC_MONETARY=German_Switzerland.1252 LC_NUMERIC=C
[5] LC_TIME=German_Switzerland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] mzR_1.3.7 Rcpp_0.9.11 devtools_0.7
loaded via a namespace (and not attached):
[1] Biobase_2.17.6 BiocGenerics_0.3.0 codetools_0.2-8 digest_0.5.2
[5] httr_0.1.1 memoise_0.1 plyr_1.7.1 RCurl_1.91-1.1
[9] stringr_0.6 tools_2.15.1
d>
Hi,
I haven't changed anything in mzR, but it seems
that the BioC build machines have recovered
from some build problems.
Can you confirm that the stock BioC packages
work for you again ? If not, I'll have to find out
what actually goes wrong next week when I am back
from travelling.
Yours,
Steffen
Updating Rcpp to 0.9.13 seems to fix the problem.
Hi,
so this implies that mzR should bump the minimum Rcpp version to 0.9.13 ?
It was Dirk Eddelbüttels interpretation that it has something got to do
with the linker flags:
http://lists.r-forge.r-project.org/pipe ... 03965.html (http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2012-June/003965.html)
Yours,
Steffen