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Topic: xcms and BiocParallel issue (Read 427 times) previous topic - next topic

  • MartijnM
  • [*]
xcms and BiocParallel issue
Hey everyone,

I have a probrlem with xcms, probably related with BiocParellel. But I can't figure it out. It used to work a few weeks ago, but my laptop crashed and installed everything (Linux, R) again from scretch. The errors are a bit hard to interpret for me. First the script and output, sessionInfo at the end. Does anybody have a clue? Thanks a lot!

The script:

library(xcms)
library(BiocParallel)

SELECTEDfiles <- list.files(wpath,pattern="(.*.mzML$)",full.names = F,recursive = T)
SELECTEDfiles

xset0 <-
  xcmsSet(
    files = SELECTEDfiles,
    profmethod = "bin",
    method = "centWave",
    ppm = 2.5,
    peakwidth = c(2, 10),
    snthresh = 10,
    noise = 25000,
    prefilter = c(2, 5000),
    integrate = 1,
    mzdiff = 0.01,
    fitgauss = F,
    sleep = 0,
    verbose.columns = FALSE
  )



gives this output:

> SELECTEDfiles    # display the files. Just for fun ;-)
 [1] "A/L049_07.mzML" "A/L049_09.mzML" "B/L049_19.mzML" "B/L049_20.mzML" "B/L049_21.mzML" "C/L049_25.mzML" "C/L049_26.mzML"
 [8] "C/L049_27.mzML" "D/L049_31.mzML" "D/L049_32.mzML" "D/L049_33.mzML" "E/L049_43.mzML" "E/L049_44.mzML" "E/L049_45.mzML"

> xset0 <-
  xcmsSet(
    files = SELECTEDfiles,
    profmethod = "bin",
    method = "centWave",
    ppm = 2.5,
    peakwidth = c(2, 10),
    snthresh = 10,
    noise = 25000,
    prefilter = c(2, 5000),
    integrate = 1,
    mzdiff = 0.01,
    fitgauss = F,
    sleep = 0,
    verbose.columns = FALSE
  )

/usr/local/lib/R/site-library/mzR/libs/mzR.so(_Z12rampOpenFilePKc+0x216)[0x7f118b976386]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(RampROpen+0x5c)[0x7f118bc38a4c]
/usr/lib/R/lib/libR.so(+0xdbb40)[0x7f11b0bdeb40]
/usr/lib/R/lib/libR.so(Rf_eval+0x789)[0x7f11b0c1c919]
/usr/lib/R/lib/libR.so(+0x11cdae)[0x7f11b0c1fdae]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
/usr/lib/R/lib/libR.so(+0x11c086)[0x7f11b0c1f086]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(R_execMethod+0x266)[0x7f11b0c22656]
/usr/lib/R/library/methods/libs/methods.so(+0x3d3b)[0x7f11a9e27d3b]
/usr/lib/R/lib/libR.so(+0x15346b)[0x7f11b0c5646b]
/usr/lib/R/lib/libR.so(+0x10ee60)[0x7f11b0c11e60]
/usr/lib/R/lib/libR.so(Rf_eval+0x198)[0x7f11b0c1c328]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(+0x10fb65)[0x7f11b0c12b65]
/usr/lib/R/lib/libR.so(Rf_eval+0x198)[0x7f11b0c1c328]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
.......
7f11aa563000-7f11aad63000 rw-p 00000000 00:00 0
7f11aad63000-7f11aad64000 ---p 00000000 00:00 0
7f11aad64000-7f11ab564000 rw-p 00000000 00:00 0
7f11ab564000-7f11ab565000 ---p 00000000 00:00 0
7f11ab565000-7f11abd65000 rw-p 00000000 00:00 0
7f11abd65000-7f11ad3d1000 r-xp 00000000 08:03 7629                      /usr/lib/x86_64-linux-gnu/libicudata.so.52.1
7f11ad3d1000-7f11ad5d0000 ---p 0166c000 08:03 7629                      /usr/lib/x86_64-linux-gnu/libicudata.so.52.1
7f11ad5d0000-7f11ad5d1000 r--p 0166b000 08:03 7629                      /usr/lib/x86_64-linux-gnu/libicudata.so.52.1
7f11ae7f5000-7f11ae7f6000 rw-p 00025000 08:03 196730                    /lib/x86_64-linux-gnu/liblzma.so.5.2.2
7f11ae7f6000-7f11ae868000 r-xp 00000000 08:03 171371                    /lib/x86_64-linux-gnu/libpcre.so.3.13.3
7f11ae868000-7f11aea67000 ---p 00072000 08:03 171371                    /lib/x86_64-linux-gnu/libpcre.so.3.13.3
7f11aea67000-7f11aea68000 r--p 00071000 08:03 171371                    /lib/x86_64-linux-gnu/libpcre.so.3.13.3
7f11aea68000-7f11aea69000 rw-p 00072000 08:03 171371                    /lib/x86_64-linux-gnu/libpcre.so.3.13.3
7f11b08f9000-7f11b08fa000 r--p 00017000 08:03 202741                    /lib/x86_64-linux-gnu/libpthread-2.24.so
7f11b08fa000-7f11b08fb000 rw-p 00018000 08:03 202741                    /lib/x86_64-linux-gnu/libpthread-2.24.so
7f11b08fb000-7f11b08ff000 rw-p 00000000 00:00 0
7f11b08ff000-7f11b0901000 r-xp 00000000 08:03 202729                    /lib/x86_64-linux-gnu/libdl-2.24.so
7f11b0901000-7f11b0b01000 ---p 00002000 08:03 202729                    /lib/x86_64-linux-gnu/libdl-2.24.so
7f11b0b01000-7f11b0b02000 r--p 00002000 08:03 202729                    /lib/x86_64-linux-gnu/libdl-2.24.so
7ffdb85ce000-7ffdb85d0000 r--p 00000000 00:00 0                          [vvar]
7ffdb85d0000-7ffdb85d2000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
/lib/x86_64-linux-gnu/libc.so.6(+0x70bcb)[0x7f11af4f5bcb]
/lib/x86_64-linux-gnu/libc.so.6(+0x76f96)[0x7f11af4fbf96]
/lib/x86_64-linux-gnu/libc.so.6(+0x7778e)[0x7f11af4fc78e]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZN4pwiz6msdata2IO13HandlerMSData12startElementERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8minimxml9SAXParser7Handler10AttributesEl+0x22d)[0x7f118bb19a8d]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(+0x50c6f3)[0x7f118bc1e6f3]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZN4pwiz8minimxml9SAXParser5parseERSiRNS1_7HandlerE+0xaad)[0x7f118bc1feed]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZN4pwiz6msdata2IO4readERSiRNS0_6MSDataENS1_16SpectrumListFlagE+0x1196)[0x7f118bb06cd6]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZNK4pwiz6msdata15Serializer_mzML4Impl4readEN5boost10shared_ptrISiEERNS0_6MSDataE+0x6b)[0x7f118ba97e6b]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZNK4pwiz6msdata15Serializer_mzML4readEN5boost10shared_ptrISiEERNS0_6MSDataE+0x3a)[0x7f118ba9850a]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZNK4pwiz6msdata11Reader_mzML4readERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RNS0_6MSDataEiRKNS0_6Reader6ConfigE+0x20c)[0x7f118ba8270c]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZNK4pwiz6msdata10ReaderList4readERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RNS0_6MSDataEiRKNS0_6Reader6ConfigE+0xb5)[0x7f118ba9e295]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(+0x41dd64)[0x7f118bb2fd64]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZN4pwiz6msdata10MSDataFileC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS0_6ReaderEb+0xda)[0x7f118bb31cda]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_ZN4pwiz6msdata11RAMPAdapterC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x2a)[0x7f118bb294aa]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(_Z12rampOpenFilePKc+0x216)[0x7f118b976386]
/usr/local/lib/R/site-library/mzR/libs/mzR.so(RampROpen+0x5c)[0x7f118bc38a4c]
/usr/lib/R/lib/libR.so(+0xdbb40)[0x7f11b0bdeb40]
/usr/lib/R/lib/libR.so(Rf_eval+0x789)[0x7f11b0c1c919]
/usr/lib/R/lib/libR.so(+0x11cdae)[0x7f11b0c1fdae]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
/usr/lib/R/lib/libR.so(+0x11c086)[0x7f11b0c1f086]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(R_execMethod+0x266)[0x7f11b0c22656]
/usr/lib/R/library/methods/libs/methods.so(+0x3d3b)[0x7f11a9e27d3b]
/usr/lib/R/lib/libR.so(+0x15346b)[0x7f11b0c5646b]
/usr/lib/R/lib/libR.so(+0x10ee60)[0x7f11b0c11e60]
/usr/lib/R/lib/libR.so(Rf_eval+0x198)[0x7f11b0c1c328]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(+0x10fb65)[0x7f11b0c12b65]
/usr/lib/R/lib/libR.so(Rf_eval+0x198)[0x7f11b0c1c328]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
/usr/lib/R/lib/libR.so(+0x11b698)[0x7f11b0c1e698]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(R_execMethod+0x266)[0x7f11b0c22656]
/usr/lib/R/library/methods/libs/methods.so(+0x3d3b)[0x7f11a9e27d3b]
/usr/lib/R/lib/libR.so(+0x15346b)[0x7f11b0c5646b]
/usr/lib/R/lib/libR.so(Rf_eval+0x6cf)[0x7f11b0c1c85f]
/usr/lib/R/lib/libR.so(+0x11f22f)[0x7f11b0c2222f]
/usr/lib/R/lib/libR.so(Rf_eval+0x34f)[0x7f11b0c1c4df]
/usr/lib/R/lib/libR.so(+0x11c086)[0x7f11b0c1f086]
/usr/lib/R/lib/libR.so(Rf_eval+0x588)[0x7f11b0c1c718]
======= Memory map: ========
00400000-013d1000 r-xp 00000000 08:03 1313112                            /usr/lib/rstudio/bin/rsession
015d0000-015ee000 r--p 00fd0000 08:03 1313112                            /usr/lib/rstudio/bin/rsession
015ee000-015f3000 rw-p 00fee000 08:03 1313112                            /usr/lib/rstudio/bin/rsession
015f3000-015fb000 rw-p 00000000 00:00 0
02254000-0c740000 rw-p 00000000 00:00 0                                  [heap]
7f1181ae5000-7f1181b21000 r-xp 00000000 08:03 397173                    /usr/local/lib/R/site-library/xcms/libs/xcms.so
7f1181b21000-7f1181d20000 ---p 0003c000 08:03 397173                    /usr/local/lib/R/site-library/xcms/libs/xcms.so
7f1181d20000-7f1181d21000 r--p 0003b000 08:03 397173                    /usr/local/lib/R/site-library/xcms/libs/xcms.so
7f1181d21000-7f1181d22000 rw-p 0003c000 08:03 397173                    /usr/local/lib/R/site-library/xcms/libs/xcms.so
7f1181d22000-7f1181d23000 r-xp 00000000 08:03 132602                    /usr/local/lib/R/site-library/MassSpecWavelet/libs/MassSpecWavelet.so
7f1181d23000-7f1181f22000 ---p 00001000 08:03 132602                    /usr/local/lib/R/site-library/MassSpecWavelet/libs/MassSpecWavelet.so
7f1181f22000-7f1181f23000 r--p 00000000 08:03 132602                    /usr/local/lib/R/site-library/MassSpecWavelet/libs/MassSpecWavelet.so
7f1181f23000-7f1181f24000 rw-p 00001000 08:03 132602                    /usr/local/lib/R/site-library/MassSpecWavelet/libs/MassSpecWavelet.so
7f1181f24000-7f1181f31000 r-xp 00000000 08:03 132376                    /usr/local/lib/R/site-library/RANN/libs/RANN.so
7f1181f31000-7f1182130000 ---p 0000d000 08:03 132376                    /usr/local/lib/R/site-library/RANN/libs/RANN.so
7f1182130000-7f1182131000 r--p 0000c000 08:03 132376                    /usr/local/lib/R/site-library/RANN/libs/RANN.so
7f1182131000-7f1182132000 rw-p 0000d000 08:03 132376                    /usr/local/lib/R/site-library/RANN/libs/RANN.so
7f1182132000-7f118213d000 r-xp 00000000 08:03 132999                    /usr/local/lib/R/site-library/multtest/libs/multtest.so
7f118213d000-7f118233d000 ---p 0000b000 08:03 132999                    /usr/local/lib/R/site-library/multtest/libs/multtest.so
7f118233d000-7f118233e000 r--p 0000b000 08:03 132999                    /usr/local/lib/R/site-library/multtest/libs/multtest.so
7f118233e000-7f118233f000 rw-p 0000c000 08:03 132999                    /usr/local/lib/R/site-library/multtest/libs/multtest.so
7f119a1aa000-7f119a1ab000 rw-p 00015000 08:03 90451                      /usr/lib/R/library/tools/libs/tools.so
7f119a1ab000-7f119ad81000 r-xp 00000000 08:03 1454077                    /usr/lib/rstudio/bin/rsclang/libclang.so
7f119ad81000-7f119af80000 ---p 00bd6000 08:03 1454077                    /usr/lib/rstudio/bin/rsclang/libclang.so
7f119af80000-7f119affa000 r--p 00bd5000 08:03 1454077                    /usr/lib/rstudio/bin/rsclang/libclang.so
7f119affa000-7f119affb000 rw-p 00c4f000 08:03 1454077                    /usr/lib/rstudio/bin/rsclang/libclang.so
7f119affb000-7f119affe000 rw-p 00000000 00:00 0
7f11a9763000-7f11a980a000 r-xp 00000000 08:03 90762                      /usr/lib/R/library/stats/libs/stats.so
7f11a980a000-7f11a9a0a000 ---p 000a7000 08:03 90762                      /usr/lib/R/library/stats/libs/stats.so
7f11a9a0a000-7f11a9a0c000 r--p 000a7000 08:03 90762                      /usr/lib/R/library/stats/libs/stats.so
7f11a9a0c000-7f11a9a0e000 rw-p 000a9000 08:03 90762                      /usr/lib/R/library/stats/libs/stats.so
7f11a9a0e000-7f11a9ae7000 rw-p 00000000 00:00 0
7f11a9ae7000-7f11a9ae9000 r-xp 00000000 08:03 6415                      /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f11a9ae9000-7f11a9ce8000 ---p 00002000 08:03 6415                      /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f11a9ce8000-7f11a9ce9000 r--p 00001000 08:03 6415                      /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f11a9ce9000-7f11a9cea000 rw-p 00002000 08:03 6415                      /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f11a9cea000-7f11a9e24000 rw-p 00000000 00:00 0
7f11a9e24000-7f11a9e2c000 r-xp 00000000 08:03 90656                      /usr/lib/R/library/methods/libs/methods.so
7f11a9e2c000-7f11aa02b000 ---p 00008000 08:03 90656                      /usr/lib/R/library/methods/libs/methods.so
7f11aa02b000-7f11aa02c000 r--p 00007000 08:03 90656                      /usr/lib/R/library/methods/libs/methods.so
7f11aa02c000-7f11aa02d000 rw-p 00008000 08:03 90656                      /usr/lib/R/library/methods/libs/methods.so
7f11aa085000-7f11aa562000 rw-p 00000000 00:00 0
7f11aa562000-7f11aa563000 ---p 00000000 00:00 0
7f11aa563000-7f11aad63000 rw-p 00000000 00:00 0
7f11aad63000-7f11aad64000 ---p 00000000 00:00 0
7f11aad64000-7f11ab564000 rw-p 00000000 00:00 0
7f11ae3bf000-7f11ae3c0000 rw-p 00007000 08:03 202743                    /lib/x86_64-linux-gnu/librt-2.24.so
7f11ae3c0000-7f11ae3cf000 r-xp 00000000 08:03 196584                    /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f11ae3cf000-7f11ae5ce000 ---p 0000f000 08:03 196584                    /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f11ae5ce000-7f11ae5cf000 r--p 0000e000 08:03 196584                    /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f11b04dd000-7f11b04de000 r--p 00003000 08:03 168536                    /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f11b1181000-7f11b131c000 r--p 00000000 08:03 877                        /usr/lib/locale/locale-archive
7f11b131c000-7f11b133a000 rw-p 00000000 00:00 0
7f11b133f000-7f11b1340000 rw-p 00000000 00:00 0
7f11b1340000-7f11b1350000 rwxp 00000000 00:00 0
7f11b1350000-7f11b1351000 r--p 00000000 08:03 93503                      /usr/lib/R/library/translations/en/LC_MESSAGES/R.mo
7f11b1351000-7f11b1358000 r--s 00000000 08:03 6717                      /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f11b1358000-7f11b135b000 rw-p 00000000 00:00 0
7f11b135b000-7f11b135c000 r--p 00023000 08:03 175976                    /lib/x86_64-linux-gnu/ld-2.24.so
7f11b135c000-7f11b135d000 rw-p 00024000 08:03 175976                    /lib/x86_64-linux-gnu/ld-2.24.so
7f11b135d000-7f11b135e000 rw-p 00000000 00:00 0
7ffdb84d9000-7ffdb8563000 rw-p 00000000 00:00 0                          [stack]
7ffdb85ce000-7ffdb85d0000 r--p 00000000 00:00 0                          [vvar]
7ffdb85d0000-7ffdb85d2000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Error: 'bplapply' receive data failed:
  error reading from connection


> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Deepin 15

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.7.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

locale:
[1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C              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    LC_PAPER=en_US.UTF-8      LC_NAME=C               
[9] LC_ADDRESS=C              LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C     

attached base packages:
[1] parallel  stats    graphics  grDevices utils    datasets  methods  base   

other attached packages:
[1] BiocParallel_1.10.1 xcms_1.50.1        Biobase_2.34.0      ProtGenerics_1.6.0  BiocGenerics_0.20.0 mzR_2.8.1         
[7] Rcpp_0.12.11     

loaded via a namespace (and not attached):
[1] RANN_2.5.1            lattice_0.20-35        codetools_0.2-15      MASS_7.3-47            MassSpecWavelet_1.40.0
[6] grid_3.4.0            plyr_1.8.4            stats4_3.4.0          S4Vectors_0.12.2      Matrix_1.2-10       
[11] splines_3.4.0          RColorBrewer_1.1-2    tools_3.4.0            survival_2.41-3        compiler_3.4.0       
[16] multtest_2.30.0 
  • PhD-student Universiteit Utrecht

  • Jan Stanstrup
  • [*][*][*][*][*]
  • Administrator
Re: xcms and BiocParallel issue
Reply #1
No clue. The first I would try is to install xcms (devel branch) and mzR from github. Your versions are a bit old and might not like each other.
  • Steno Diabetes Center Copenhagen, Denmark
Blog: stanstrup.github.io