[BioC] one problem about IRanges Package

Vincent Carey stvjc at channing.harvard.edu
Thu Nov 11 05:02:47 CET 2010 

You are welcome.  In future please carbon the main list so that the
knowledge of the solution may be shared.

On Wed, Nov 10, 2010 at 10:51 PM, cao zongfu <caozongfu at gmail.com> wrote:
> Thank you for your help.There is no more any errro. I have suceeded.
>
> 2010/11/10, Vincent Carey <stvjc at channing.harvard.edu>:
>> you need to restart R.  try that and do library(gcrma) and tell me if
>> you still see an error
>>
>> On Wed, Nov 10, 2010 at 2:13 AM, cao zongfu <caozongfu at gmail.com> wrote:
>>> Dear Prof.,
>>>     I am sorry to troble you again. I have checked the IRanges path,
>>> I found that it  maybe because the file 'IRanges.dll' missing, which
>>> should be in the path of '.\Program
>>> Files\R\R-2.12.0\library\IRanges\libs\x64', not in the path of
>>> '.\Program Files\R\R-2.12.0\library\IRanges\libs\i386'. Would you
>>> please send me the file? I'd like to try again. I think if I get the
>>> file, I will be suceed.
>>>     Thank you again.
>>>
>>> Cao Zongfu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> 2010/11/10, cao zongfu <caozongfu at gmail.com>:
>>>> Dear Prof.,
>>>>       I have installed R2.12.0 on personal computer, and use
>>>> biocLite() toinstall the packages simpleaffy,but I failed again.
>>>> ‘IRanges’ is not available yet.Some details are as follows
>>>>
>>>>
>>>>> source("http://bioconductor.org/biocLite.R")
>>>> BioC_mirror = http://www.bioconductor.org
>>>> Change using chooseBioCmirror().
>>>>> biocLite("simpleaffy")
>>>> Using R version 2.12.0, biocinstall version 2.7.4.
>>>> Installing Bioconductor version 2.7 packages:
>>>> [1] "simpleaffy"
>>>> Please wait...
>>>>
>>>> Warning: dependency ‘IRanges’ is not available
>>>> also installing the dependencies ‘DBI’, ‘RSQLite’, ‘xtable’, ‘affyio’,
>>>> ‘preprocessCore’, ‘AnnotationDbi’, ‘annotate’, ‘Biostrings’, ‘affy’,
>>>> ‘genefilter’, ‘Biobase’, ‘gcrma’
>>>>
>>>> trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/DBI_0.2-5.zip'
>>>> Content type 'application/zip' length 386424 bytes (377 Kb)
>>>> opened URL
>>>> downloaded 377 Kb
>>>>
>>>> trying URL
>>>> 'http://cran.fhcrc.org/bin/windows/contrib/2.12/RSQLite_0.9-3.zip'
>>>> Content type 'application/zip' length 978646 bytes (955 Kb)
>>>> opened URL
>>>> downloaded 955 Kb
>>>>
>>>> trying URL
>>>> 'http://cran.fhcrc.org/bin/windows/contrib/2.12/xtable_1.5-6.zip'
>>>> Content type 'application/zip' length 178958 bytes (174 Kb)
>>>> opened URL
>>>> downloaded 174 Kb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/affyio_1.18.0.zip'
>>>> Content type 'application/zip' length 152256 bytes (148 Kb)
>>>> opened URL
>>>> downloaded 148 Kb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/preprocessCore_1.12.0.zip'
>>>> Content type 'application/zip' length 180568 bytes (176 Kb)
>>>> opened URL
>>>> downloaded 176 Kb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/AnnotationDbi_1.12.0.zip'
>>>> Content type 'application/zip' length 5267008 bytes (5.0 Mb)
>>>> opened URL
>>>> downloaded 5.0 Mb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/annotate_1.28.0.zip'
>>>> Content type 'application/zip' length 2210479 bytes (2.1 Mb)
>>>> opened URL
>>>> downloaded 2.1 Mb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/Biostrings_2.18.0.zip'
>>>> Content type 'application/zip' length 2360722 bytes (2.3 Mb)
>>>> opened URL
>>>> downloaded 2.3 Mb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/affy_1.28.0.zip'
>>>> Content type 'application/zip' length 2067173 bytes (2.0 Mb)
>>>> opened URL
>>>> downloaded 2.0 Mb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/genefilter_1.32.0.zip'
>>>> Content type 'application/zip' length 965461 bytes (942 Kb)
>>>> opened URL
>>>> downloaded 942 Kb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/Biobase_2.10.0.zip'
>>>> Content type 'application/zip' length 2594549 bytes (2.5 Mb)
>>>> opened URL
>>>> downloaded 2.5 Mb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/gcrma_2.22.0.zip'
>>>> Content type 'application/zip' length 236187 bytes (230 Kb)
>>>> opened URL
>>>> downloaded 230 Kb
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/simpleaffy_2.26.0.zip'
>>>> Content type 'application/zip' length 804264 bytes (785 Kb)
>>>> opened URL
>>>> downloaded 785 Kb
>>>>
>>>> package 'DBI' successfully unpacked and MD5 sums checked
>>>> package 'RSQLite' successfully unpacked and MD5 sums checked
>>>> package 'xtable' successfully unpacked and MD5 sums checked
>>>> package 'affyio' successfully unpacked and MD5 sums checked
>>>> package 'preprocessCore' successfully unpacked and MD5 sums checked
>>>> package 'AnnotationDbi' successfully unpacked and MD5 sums checked
>>>> package 'annotate' successfully unpacked and MD5 sums checked
>>>> package 'Biostrings' successfully unpacked and MD5 sums checked
>>>> package 'affy' successfully unpacked and MD5 sums checked
>>>> package 'genefilter' successfully unpacked and MD5 sums checked
>>>> package 'Biobase' successfully unpacked and MD5 sums checked
>>>> package 'gcrma' successfully unpacked and MD5 sums checked
>>>> package 'simpleaffy' successfully unpacked and MD5 sums checked
>>>>
>>>> The downloaded packages are in
>>>>         C:\Documents and Settings\Administrator\Local
>>>> Settings\Temp\Rtmp1Ycqzb\downloaded_packages
>>>>> library(simpleaffy)
>>>> Loading required package: affy
>>>> Loading required package: Biobase
>>>>
>>>> Welcome to Bioconductor
>>>>
>>>>   Vignettes contain introductory material. To view, type
>>>>   'openVignette()'. To cite Bioconductor, see
>>>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>>
>>>> Loading required package: genefilter
>>>> Loading required package: gcrma
>>>> Error in loadNamespace(i, c(lib.loc, .libPaths())) :
>>>>   there is no package called 'IRanges'
>>>> Error: package 'gcrma' could not be loaded
>>>>> biocLite("gcrma")
>>>> Using R version 2.12.0, biocinstall version 2.7.4.
>>>> Installing Bioconductor version 2.7 packages:
>>>> [1] "gcrma"
>>>> Please wait...
>>>>
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/gcrma_2.22.0.zip'
>>>> Content type 'application/zip' length 236187 bytes (230 Kb)
>>>> opened URL
>>>> downloaded 230 Kb
>>>>
>>>> package 'gcrma' successfully unpacked and MD5 sums checked
>>>>
>>>> The downloaded packages are in
>>>>         C:\Documents and Settings\Administrator\Local
>>>> Settings\Temp\Rtmp1Ycqzb\downloaded_packages
>>>>> library(gcrma)
>>>> Error in loadNamespace(i, c(lib.loc, .libPaths())) :
>>>>   there is no package called 'IRanges'
>>>> Error: package/namespace load failed for 'gcrma'
>>>>> biocLite("IRanges")
>>>> Using R version 2.12.0, biocinstall version 2.7.4.
>>>> Installing Bioconductor version 2.7 packages:
>>>> [1] "IRanges"
>>>> Please wait...
>>>>
>>>> Warning message:
>>>> In getDependencies(pkgs, dependencies, available, lib) :
>>>>   package ‘IRanges’ is not available
>>>>> sessionInfo()
>>>> R version 2.12.0 (2010-10-15)
>>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>>>> States.1252    LC_MONETARY=English_United States.1252
>>>> [4] LC_NUMERIC=C                           LC_TIME=English_United
>>>> States.1252
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] genefilter_1.32.0 affy_1.28.0       Biobase_2.10.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>>  [1] affyio_1.18.0         annotate_1.28.0       AnnotationDbi_1.12.0
>>>> DBI_0.2-5             preprocessCore_1.12.0
>>>>  [6] RSQLite_0.9-3         splines_2.12.0        survival_2.35-8
>>>> tools_2.12.0          xtable_1.5-6
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2010/11/9, Vincent Carey <stvjc at channing.harvard.edu>:
>>>>> Dr Zongfu:
>>>>>
>>>>> It will be easier to help you if you will use updated resources.
>>>>> Please install R 2.12, the current version, and then use biocLite() to
>>>>> install the packages you need.  After this if you find an error,
>>>>> please send all details to the list.  I personally maintain a 64 bit
>>>>> windows 7 (not XP) machine so may not be able to reproduce your
>>>>> situation well.  It would be advisable to use windows 7 if available.
>>>>>
>>>>> On Mon, Nov 8, 2010 at 11:56 PM, cao zongfu <caozongfu at gmail.com> wrote:
>>>>>> Dear Prof. , Hi
>>>>>>
>>>>>>       I am a R user from National Engineering Research Center for
>>>>>> Beijing Biochip Technology  of China. Recently, I used simpleaffy
>>>>>> package to perform quality control of Affymetrix expression profile
>>>>>> chip. I met one problem:
>>>>>>
>>>>>>       I found that simpleaffy can not work under R2.11.1-X64 on my
>>>>>> computer. As we known, IRanges was used in the simpleaffy package. I
>>>>>> used R2.11.1-X64 under 64-bit Windows XP. I found that IRanges 1.8.2
>>>>>> can not work.When I used library(IRanges) command, the error said:
>>>>>> package "Iranges" is not install for the 'arch=x64'. But I have
>>>>>> install the IRanges into the R in deed. I want to know  whether the
>>>>>> simpleaffy can only work under the R32. If I hope to used the R64 in
>>>>>> order to increasing the efficiency, Would you please help me how to
>>>>>> deal with?Thank you in advance.
>>>>>>
>>>>>>
>>>>>> R version 2.11.1 (2010-05-31)
>>>>>> x86_64-pc-mingw32
>>>>>>
>>>>>> locale:
>>>>>> [1] LC_COLLATE=Chinese_People's Republic of China.936
>>>>>> LC_CTYPE=Chinese_People's Republic of China.936
>>>>>> [3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C
>>>>>> [5] LC_TIME=Chinese_People's Republic of China.936
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] genefilter_1.30.0 affy_1.26.1       Biobase_2.8.0
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>>  [1] affyio_1.16.0         annotate_1.28.0       AnnotationDbi_1.12.0
>>>>>> DBI_0.2-5             preprocessCore_1.10.0
>>>>>>  [6] RSQLite_0.9-2         splines_2.11.1        survival_2.35-8
>>>>>> tools_2.11.1          xtable_1.5-6
>>>>>>>        library(IRanges)
>>>>>> error: Package "Iranges" is not install for the 'arch=x64'.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Zongfu Cao
>>>>>>
>>>>>> National Engineering Research Center for Beijing Biochip Technology  of
>>>>>> China
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>
>>>
>>
>

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