[BioC] PICS

Fri Oct 21 19:44:02 CEST 2011

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/libs/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/libs/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 à 13:27, Zhu, Lihua (Julie) a écrit :
> 
>> 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 à 09:39, Zhu, Lihua (Julie) a écrit :
>>> 
>>>> 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/libs/x>>>>
8
>>>> 6_64/PICS.so
>>>> Expected in: dynamic lookup
>>>> 
>>>> Error: package/namespace load failed for ŒPICS¹
>>>> 
>>>> 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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>>> 
>>> 
>> 
> 
> 