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xcms & mzR installation problem

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
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
>

Re: xcms & mzR installation problem

Reply #1
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
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

Re: xcms & mzR installation problem

Reply #2
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

Re: xcms & mzR installation problem

Reply #3
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 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 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.

Re: xcms & mzR installation problem

Reply #4
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

Code: [Select]
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.
Code: [Select]
> 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:
Code: [Select]
> 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:
Code: [Select]
> 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.

Re: xcms & mzR installation problem

Reply #5
I can confirm this. A bug report was sent to the mzR developers.

Ralf

Re: xcms & mzR installation problem

Reply #6
Building from source worked, btw.

Re: xcms & mzR installation problem

Reply #7
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
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

 

Re: xcms & mzR installation problem

Reply #8
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


Code: [Select]
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>

Re: xcms & mzR installation problem

Reply #9
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
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

Re: xcms & mzR installation problem

Reply #10
Updating Rcpp to 0.9.13 seems to fix the problem.

Re: xcms & mzR installation problem

Reply #11
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

Yours,
Steffen
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE