PICS
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 5 months ago
United States
Dear PICS developers, I encountered problem loading PICS Version: 1.7.0. Could you please let me know how to fix this? Many thanks! Best regards, Julie library(PICS) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS/ libs/x 86_64/PICS.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library /PICS/ libs/x86_64/PICS.so, 6): Symbol not found: _gsl_blas_dgemv Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS/l ibs/x8 6_64/PICS.so Expected in: dynamic lookup Error: package/namespace load failed for ?PICS? sessionInfo() R version 2.14.0 beta (2011-10-17 r57293) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_2.0.5 gplots_2.10.1 [3] KernSmooth_2.23-6 caTools_1.12 [5] bitops_1.0-4.1 gdata_2.8.2 [7] gtools_2.6.2 limma_3.9.22 [9] org.Hs.eg.db_2.6.3 GO.db_2.6.1 [11] RSQLite_0.10.0 DBI_0.2-5 [13] AnnotationDbi_1.15.38 BSgenome.Ecoli.NCBI.20080805_1.3.17 [15] multtest_2.9.1 Biobase_2.13.11 [17] biomaRt_2.9.3 BiocInstaller_1.1.28 [19] ShortRead_1.11.44 latticeExtra_0.6-18 [21] RColorBrewer_1.0-5 Rsamtools_1.5.76 [23] lattice_0.19-33 BSgenome_1.21.7 [25] Biostrings_2.21.11 GenomicRanges_1.5.51 [27] IRanges_1.11.31 loaded via a namespace (and not attached): [1] hwriter_1.3 MASS_7.3-16 RCurl_1.6-10 rtracklayer_1.13.19 splines_2.14.0 [6] survival_2.36-10 tools_2.14.0 XML_3.4-3 zlibbioc_0.1.8
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Arnaud Droit ▴ 20
@arnaud-droit-4921
Last seen 8.4 years ago
Hi Julie, It seems a problems with GSL. Have you GSL installed on your environment ? Thanks, Arnaud. Le 2011-10-21 ? 09:39, Zhu, Lihua (Julie) a ?crit : > Dear PICS developers, > > I encountered problem loading PICS Version: 1.7.0. Could you please let me > know how to fix this? > > Many thanks! > > Best regards, > > Julie > > library(PICS) > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/PIC S/libs/x > 86_64/PICS.so': > > dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/libra ry/PICS/ > libs/x86_64/PICS.so, 6): Symbol not found: _gsl_blas_dgemv > Referenced from: > /Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS /libs/x8 > 6_64/PICS.so > Expected in: dynamic lookup > > Error: package/namespace load failed for ?PICS? > > sessionInfo() > R version 2.14.0 beta (2011-10-17 r57293) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] ChIPpeakAnno_2.0.5 gplots_2.10.1 > [3] KernSmooth_2.23-6 caTools_1.12 > [5] bitops_1.0-4.1 gdata_2.8.2 > [7] gtools_2.6.2 limma_3.9.22 > [9] org.Hs.eg.db_2.6.3 GO.db_2.6.1 > [11] RSQLite_0.10.0 DBI_0.2-5 > [13] AnnotationDbi_1.15.38 BSgenome.Ecoli.NCBI.20080805_1.3.17 > [15] multtest_2.9.1 Biobase_2.13.11 > [17] biomaRt_2.9.3 BiocInstaller_1.1.28 > [19] ShortRead_1.11.44 latticeExtra_0.6-18 > [21] RColorBrewer_1.0-5 Rsamtools_1.5.76 > [23] lattice_0.19-33 BSgenome_1.21.7 > [25] Biostrings_2.21.11 GenomicRanges_1.5.51 > [27] IRanges_1.11.31 > > loaded via a namespace (and not attached): > [1] hwriter_1.3 MASS_7.3-16 RCurl_1.6-10 > rtracklayer_1.13.19 splines_2.14.0 > [6] survival_2.36-10 tools_2.14.0 XML_3.4-3 > zlibbioc_0.1.8 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 5 months ago
United States
Arnaud, Many thanks for your quick response and suggestions. After GSL and snowfall installation, PICS can be loaded in R 32-bit environment. However it cannot be loaded to R 64-bit environment ( x86_64-apple-darwin9.8.0/x86_64). Is this expected? Thanks! Best regards, Julie On 10/21/11 9:43 AM, "Arnaud Droit" <arnaud.droit at="" crchuq.ulaval.ca=""> wrote: > Hi Julie, > > It seems a problems with GSL. > Have you GSL installed on your environment ? > > Thanks, > > Arnaud. > > Le 2011-10-21 ? 09:39, Zhu, Lihua (Julie) a ?crit : > >> Dear PICS developers, >> >> I encountered problem loading PICS Version: 1.7.0. Could you please let me >> know how to fix this? >> >> Many thanks! >> >> Best regards, >> >> Julie >> >> library(PICS) >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/PI CS/libs/x >> 86_64/PICS.so': >> >> dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/libr ary/PICS/ >> libs/x86_64/PICS.so, 6): Symbol not found: _gsl_blas_dgemv >> Referenced from: >> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/PIC S/libs/x8 >> 6_64/PICS.so >> Expected in: dynamic lookup >> >> Error: package/namespace load failed for ?PICS? >> >> sessionInfo() >> R version 2.14.0 beta (2011-10-17 r57293) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] ChIPpeakAnno_2.0.5 gplots_2.10.1 >> [3] KernSmooth_2.23-6 caTools_1.12 >> [5] bitops_1.0-4.1 gdata_2.8.2 >> [7] gtools_2.6.2 limma_3.9.22 >> [9] org.Hs.eg.db_2.6.3 GO.db_2.6.1 >> [11] RSQLite_0.10.0 DBI_0.2-5 >> [13] AnnotationDbi_1.15.38 BSgenome.Ecoli.NCBI.20080805_1.3.17 >> [15] multtest_2.9.1 Biobase_2.13.11 >> [17] biomaRt_2.9.3 BiocInstaller_1.1.28 >> [19] ShortRead_1.11.44 latticeExtra_0.6-18 >> [21] RColorBrewer_1.0-5 Rsamtools_1.5.76 >> [23] lattice_0.19-33 BSgenome_1.21.7 >> [25] Biostrings_2.21.11 GenomicRanges_1.5.51 >> [27] IRanges_1.11.31 >> >> loaded via a namespace (and not attached): >> [1] hwriter_1.3 MASS_7.3-16 RCurl_1.6-10 >> rtracklayer_1.13.19 splines_2.14.0 >> [6] survival_2.36-10 tools_2.14.0 XML_3.4-3 >> zlibbioc_0.1.8 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Hi Julie, It should works also on R-64 environment. Could you send me the error message and R session ? I am using the same config (Apple 64 bit) as you. Arnaud. Le 2011-10-21 ? 13:27, Zhu, Lihua (Julie) a ?crit : > Arnaud, > > Many thanks for your quick response and suggestions. After GSL and snowfall > installation, PICS can be loaded in R 32-bit environment. However it cannot > be loaded to R 64-bit environment ( x86_64-apple- darwin9.8.0/x86_64). Is > this expected? Thanks! > > Best regards, > > Julie > > > On 10/21/11 9:43 AM, "Arnaud Droit" <arnaud.droit at="" crchuq.ulaval.ca=""> wrote: > >> Hi Julie, >> >> It seems a problems with GSL. >> Have you GSL installed on your environment ? >> >> Thanks, >> >> Arnaud. >> >> Le 2011-10-21 ? 09:39, Zhu, Lihua (Julie) a ?crit : >> >>> Dear PICS developers, >>> >>> I encountered problem loading PICS Version: 1.7.0. Could you please let me >>> know how to fix this? >>> >>> Many thanks! >>> >>> Best regards, >>> >>> Julie >>> >>> library(PICS) >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> unable to load shared object >>> '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/P ICS/libs/x >>> 86_64/PICS.so': >>> >>> dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/lib rary/PICS/ >>> libs/x86_64/PICS.so, 6): Symbol not found: _gsl_blas_dgemv >>> Referenced from: >>> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/PI CS/libs/x8 >>> 6_64/PICS.so >>> Expected in: dynamic lookup >>> >>> Error: package/namespace load failed for ?PICS? >>> >>> sessionInfo() >>> R version 2.14.0 beta (2011-10-17 r57293) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] ChIPpeakAnno_2.0.5 gplots_2.10.1 >>> [3] KernSmooth_2.23-6 caTools_1.12 >>> [5] bitops_1.0-4.1 gdata_2.8.2 >>> [7] gtools_2.6.2 limma_3.9.22 >>> [9] org.Hs.eg.db_2.6.3 GO.db_2.6.1 >>> [11] RSQLite_0.10.0 DBI_0.2-5 >>> [13] AnnotationDbi_1.15.38 BSgenome.Ecoli.NCBI.20080805_1.3.17 >>> [15] multtest_2.9.1 Biobase_2.13.11 >>> [17] biomaRt_2.9.3 BiocInstaller_1.1.28 >>> [19] ShortRead_1.11.44 latticeExtra_0.6-18 >>> [21] RColorBrewer_1.0-5 Rsamtools_1.5.76 >>> [23] lattice_0.19-33 BSgenome_1.21.7 >>> [25] Biostrings_2.21.11 GenomicRanges_1.5.51 >>> [27] IRanges_1.11.31 >>> >>> loaded via a namespace (and not attached): >>> [1] hwriter_1.3 MASS_7.3-16 RCurl_1.6-10 >>> rtracklayer_1.13.19 splines_2.14.0 >>> [6] survival_2.36-10 tools_2.14.0 XML_3.4-3 >>> zlibbioc_0.1.8 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >
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Arnaud, The makeRangedDataOutput outputs null when it should output a RangedData object with peaks having score >=2. Here is the example you ran in Bioc2011 for ER dataset. Did I miss something? Thanks! Best regards, Julie RD <- as(pics, "RangedData") RD RangedData with 304 rows and 1 value column across 2 spaces space ranges | score <factor> <iranges> | <numeric> pics1 chr21 [42669615, 42669741] | 98.27149 pics2 chr21 [42659913, 42660054] | 88.79954 pics3 chr21 [41898880, 41899010] | 85.83956 pics4 chr21 [45574708, 45574826] | 81.39958 pics5 chr21 [45631173, 45631311] | 79.91959 pics8 chr21 [15504544, 15504699] | 59.93969 pics11 chr21 [42659615, 42659758] | 46.61976 pics12 chr21 [15299644, 15299796] | 46.12643 pics13 chr21 [39208579, 39208729] | 43.65977 ... ... ... ... ... pics292 chr22 [33122494, 33122758] | 1.874657 pics293 chr22 [43400868, 43401220] | 1.849990 pics294 chr22 [38733327, 38733569] | 1.553992 pics298 chr22 [14702383, 14702743] | 1.479992 pics299 chr22 [17040892, 17041186] | 1.479992 pics300 chr22 [22827324, 22827654] | 1.479992 pics302 chr22 [15229177, 15229465] | 1.331993 pics303 chr22 [15233278, 15233637] | 1.257994 pics304 chr22 [15231777, 15232120] | 1.109994 myFilter <- list(score=c(2, Inf), delta=c(50, 300), se=c(0,50)) RD <-makeRangedDataOutput(pics, type="bed", filter=myFilter) RD null R version 2.14.0 beta (2011-10-17 r57293) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] ChipSeq_1.0.0 MotIV_1.7.0 rGADEM_2.1.0 seqLogo_1.19.0 BiocInstaller_1.1.28 [6] snowfall_1.84 snow_0.3-7 PICS_1.7.0 BSgenome_1.21.7 Biostrings_2.21.11 [11] GenomicRanges_1.5.51 IRanges_1.11.31 loaded via a namespace (and not attached): [1] lattice_0.19-33 tools_2.14.0
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 5 months ago
United States
Arnaud, Here is the output. Thanks! Julie R --arch=x86_64 CMD install PICS * installing to library ?/Library/Frameworks/R.framework/Versions/2.14/Resources/library? * installing *source* package ?PICS? ... checking for pkg-config... no checking for GSL... checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99 checking for C compiler default output file name... rm: a.out.dSYM: is a directory a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed checking for gsl-config... /usr/local/bin/gsl-config checking for GSL - version >= 1.6... yes configure: creating ./config.status config.status: creating src/Makevars ** libs *** arch - x86_64 make: Nothing to be done for `all'. installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS/l ibs/x8 6_64 ** R ** inst ** preparing package for lazy loading in method for ?as.list? with signature ?"AlignedRead"?: no definition for class ?AlignedRead? in method for ?coerce? with signature ?"AlignedRead","GenomeData"?: no definition for class ?AlignedRead? Creating a generic function for ?density? from package ?stats? in package ?PICS? Creating a generic function for ?plot? from package ?graphics? in package ?PICS? ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... ?PICS.Rnw? ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS/ libs/x 86_64/PICS.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library /PICS/ libs/x86_64/PICS.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS/l ibs/x8 6_64/PICS.so: mach-o, but wrong architecture Error: loading failed Execution halted ERROR: loading failed * removing ?/Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS? * restoring previous ?/Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS? On 10/21/11 1:29 PM, "Arnaud BioC" <arnaud.droit at="" gmail.com=""> wrote: > Hi Julie, > > It should works also on R-64 environment. > Could you send me the error message and R session ? > I am using the same config (Apple 64 bit) as you. > > Arnaud. > > > Le 2011-10-21 ? 13:27, Zhu, Lihua (Julie) a ?crit : > >> Arnaud, >> >> Many thanks for your quick response and suggestions. After GSL and snowfall >> installation, PICS can be loaded in R 32-bit environment. However it cannot >> be loaded to R 64-bit environment ( x86_64-apple- darwin9.8.0/x86_64). Is >> this expected? Thanks! >> >> Best regards, >> >> Julie >> >> >> On 10/21/11 9:43 AM, "Arnaud Droit" <arnaud.droit at="" crchuq.ulaval.ca=""> wrote: >> >>> Hi Julie, >>> >>> It seems a problems with GSL. >>> Have you GSL installed on your environment ? >>> >>> Thanks, >>> >>> Arnaud. >>> >>> Le 2011-10-21 ? 09:39, Zhu, Lihua (Julie) a ?crit : >>> >>>> Dear PICS developers, >>>> >>>> I encountered problem loading PICS Version: 1.7.0. Could you please let me >>>> know how to fix this? >>>> >>>> Many thanks! >>>> >>>> Best regards, >>>> >>>> Julie >>>> >>>> library(PICS) >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> unable to load shared object >>>> '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS/ libs/>>>> x >>>> 86_64/PICS.so': >>>> >>>> dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library /PICS>>>> / >>>> libs/x86_64/PICS.so, 6): Symbol not found: _gsl_blas_dgemv >>>> Referenced from: >>>> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/PICS/l ibs/x>>>> 8 >>>> 6_64/PICS.so >>>> Expected in: dynamic lookup >>>> >>>> Error: package/namespace load failed for ?PICS? >>>> >>>> sessionInfo() >>>> R version 2.14.0 beta (2011-10-17 r57293) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] grid stats graphics grDevices utils datasets methods >>>> base >>>> >>>> other attached packages: >>>> [1] ChIPpeakAnno_2.0.5 gplots_2.10.1 >>>> [3] KernSmooth_2.23-6 caTools_1.12 >>>> [5] bitops_1.0-4.1 gdata_2.8.2 >>>> [7] gtools_2.6.2 limma_3.9.22 >>>> [9] org.Hs.eg.db_2.6.3 GO.db_2.6.1 >>>> [11] RSQLite_0.10.0 DBI_0.2-5 >>>> [13] AnnotationDbi_1.15.38 >>>> BSgenome.Ecoli.NCBI.20080805_1.3.17 >>>> [15] multtest_2.9.1 Biobase_2.13.11 >>>> [17] biomaRt_2.9.3 BiocInstaller_1.1.28 >>>> [19] ShortRead_1.11.44 latticeExtra_0.6-18 >>>> [21] RColorBrewer_1.0-5 Rsamtools_1.5.76 >>>> [23] lattice_0.19-33 BSgenome_1.21.7 >>>> [25] Biostrings_2.21.11 GenomicRanges_1.5.51 >>>> [27] IRanges_1.11.31 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] hwriter_1.3 MASS_7.3-16 RCurl_1.6-10 >>>> rtracklayer_1.13.19 splines_2.14.0 >>>> [6] survival_2.36-10 tools_2.14.0 XML_3.4-3 >>>> zlibbioc_0.1.8 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> > >
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