[BioC] Rsubread crashes in 32bit linux
Wei Shi
shi at wehi.EDU.AU
Wed Jun 6 14:47:17 CEST 2012
Dear Dan,
Thanks a lot for the information.
The final step of the gcc compilation, which will link all the object files and creates the dynamic library Rsubread.so, should not have a large consumption of the memory and should be done fairly quick. So there seems to a problem with this step. Which Linux distribution are you running on your laptop?
Would you please install a C version of the subread aligner onto your laptop? This will be able to figure out it is C or R which caused the problem. The C version can be downloaded from http://subread.sourceforge.net
Thanks,
Wei
On Jun 6, 2012, at 9:08 PM, Dan Du wrote:
> Dear Wei,
>
> Here is a standard bioclite update, I think it is at the last step when
> compiling Rsubread.so, the memory usage exceeds 5.5g, then system freeze
> and I have to call it off. Same result when runing 'R CMD INSTALL
> Rsubread_1.6.3.tar.gz' from shell, or manually compile all .c file and
> run the last gcc statement. I guess there might just be a minimum ram
> requirement somewhere higher than 6g... I will do some more poking when
> I have time.
>
> 'gcc -std=gnu99 -shared -o Rsubread.so R_wrapper.o SNP_calling.o
> aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o
> exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o
> gene-value-index.o hashtable.o index-builder.o input-files.o
> processExons.o propmapped.o qualityScores.o readSummary.o
> removeDuplicatedReads.o sam2bed.o sorted-hashtable.o -lpthread
> -DMAKE_FOR_EXON -L/usr/lib64/R/lib -lR'
>
> Also down there are the sessionInfo and full gcc version, please let me
> know if you need more information.
>
> Regards,
> Dan
> --------------------------------------------------------------------
>> source('http://www.bioconductor.org/biocLite.R')
>> biocLite('')
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.6.
> Installing package(s) ''
> Old packages: 'Rsubread'
> Update all/some/none? [a/s/n]: a
> trying URL
> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rsubread_1.6.3.tar.gz'
> Content type 'application/x-gzip' length 21891723 bytes (20.9 Mb)
> opened URL
> ==================================================
> downloaded 20.9 Mb
>
> WARNING: ignoring environment value of R_HOME
> * installing *source* package ‘Rsubread’ ...
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c R_wrapper.c -o R_wrapper.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c SNP_calling.c -o SNP_calling.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c aligner.c -o aligner.o
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c atgcContent.c -o atgcContent.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c detectionCall.c -o detectionCall.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c detectionCallAnnotation.c -o detectionCallAnnotation.o
> detectionCallAnnotation.c: In function ‘calculateExonGCContent’:
> detectionCallAnnotation.c:175: warning: ignoring return value of
> ‘fgets’, declared with attribute warn_unused_result
> detectionCallAnnotation.c: In function ‘calculateIRGCContent’:
> detectionCallAnnotation.c:262: warning: ignoring return value of
> ‘fgets’, declared with attribute warn_unused_result
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c exon-algorithms.c -o exon-algorithms.o
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c exon-align.c -o exon-align.o
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c fullscan.c -o fullscan.o
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c gene-algorithms.c -o gene-algorithms.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c gene-value-index.c -o gene-value-index.o
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c hashtable.c -o hashtable.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c index-builder.c -o index-builder.o
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c input-files.c -o input-files.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c processExons.c -o processExons.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c propmapped.c -o propmapped.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c qualityScores.c -o qualityScores.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c readSummary.c -o readSummary.o
> readSummary.c: In function ‘readSummary’:
> readSummary.c:122: warning: format ‘%d’ expects type ‘int’, but argument
> 5 has type ‘long int’
> readSummary.c:122: warning: format ‘%d’ expects type ‘int’, but argument
> 6 has type ‘long int’
> readSummary.c:39: warning: ignoring return value of ‘getline’, declared
> with attribute warn_unused_result
> readSummary.c:52: warning: ignoring return value of ‘getline’, declared
> with attribute warn_unused_result
> readSummary.c:55: warning: ignoring return value of ‘getline’, declared
> with attribute warn_unused_result
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c removeDuplicatedReads.c -o removeDuplicatedReads.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c sam2bed.c -o sam2bed.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DMAKE_FOR_EXON -fpic
> -O3 -pipe -g -c sorted-hashtable.c -o sorted-hashtable.o
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gene-algorithms.h:23: warning: inline function ‘add_gene_vote_weighted’
> declared but never defined
> gene-algorithms.h:22: warning: inline function ‘add_gene_vote’ declared
> but never defined
> gcc -std=gnu99 -shared -o Rsubread.so R_wrapper.o SNP_calling.o
> aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o
> exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o
> gene-value-index.o hashtable.o index-builder.o input-files.o
> processExons.o propmapped.o qualityScores.o readSummary.o
> removeDuplicatedReads.o sam2bed.o sorted-hashtable.o -lpthread
> -DMAKE_FOR_EXON -L/usr/lib64/R/lib -lR
> ^Cmake: *** Deleting file `Rsubread.so'
> make: *** [Rsubread.so] Interrupt
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ‘Rsubread.Rnw’
> ** testing if installed package can be loaded
> Error in library.dynam(lib, package, package.lib) :
> shared object ‘Rsubread.so’ not found
> Error: loading failed
> Execution halted
> --------------------------------------------------------------------
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> --------------------------------------------------------------------
> $ gcc -v
> Using built-in specs.
> Target: x86_64-linux-gnu
> Configured with: ../src/configure -v --with-pkgversion='Ubuntu
> 4.4.3-4ubuntu5.1'
> --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
> --enable-shared --enable-multiarch --enable-linker-build-id
> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
> --program-suffix=-4.4 --enable-nls --enable-clocale=gnu
> --enable-libstdcxx-debug --enable-plugin --enable-objc-gc
> --disable-werror --with-arch-32=i486 --with-tune=generic
> --enable-checking=release --build=x86_64-linux-gnu
> --host=x86_64-linux-gnu --target=x86_64-linux-gnu
> Thread model: posix
> gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1)
> --------------------------------------------------------------------
>
> On Wed, 2012-06-06 at 20:10 +1000, Wei Shi wrote:
>> Dear Dan,
>>
>> It didn't seem to be problem of requesting a continuous 1GB block in our
>> investigation. We tracked the memory usage of buildindex() function when
>> running it on yeast genome using a 32-bit VM, and found that the segfault
>> happened right after a request of a few KB of memory was sent to the
>> system when the memory parameter was set to 2500. However, the problem was
>> gone when the memory parameter was changed to 1000.
>>
>> Removing highly repetitive 16 mers required a continuous 1GB block of
>> memory, but this step was always executed successfully. This step also
>> included in the old version of Rsubread (1.1.1), and it did not have
>> problem there either.
>>
>> Could you please provide us your complete code for running your test and
>> also session info? This will help us to diagnose what the problem could be
>> because we couldn't reproduce what you saw from our end.
>>
>> For the compilation issue on your 64bit laptop, could you provide us more
>> details as well, including the message output from gcc?
>>
>> Thanks,
>> Wei
>>
>>> Dear Wei,
>>>
>>> Unfortunately reducing the memory parameter to 1000, still causes the
>>> segfault. I guess with 3g ram limit on a 32bit system, there is still a
>>> fat chance that you can not request a continuous 1g block.
>>>
>>> For that 64bit laptop, it is still strange about the 6g memory draining.
>>> It is happing during the installation when compiling the shared library
>>> Rsubread.so, not running the buildindex function. Btw, the gcc version
>>> is 4.4.3.
>>>
>>> Server and opensuse box runs gcc version 4.3.1 and 4.5.0 respectively.
>>>
>>> Regards,
>>> Dan
>>>
>>> On Wed, 2012-06-06 at 14:56 +1000, Wei Shi wrote:
>>>> Dear Dan,
>>>>
>>>> It is probably because including genome sequences into the index slowed
>>>> down your laptop. But I believe it should be alleviated if you give
>>>> smaller values to the 'memory ' parameter of the buildindex() function.
>>>> Also, the index building is an one-off operation, you do not need to
>>>> redo it even when new releases come.
>>>>
>>>> For your 32-bit opensuse box, I guess the problem will be solved if you
>>>> change the amount of memory requested to be 1000MB.
>>>>
>>>> Cheers,
>>>> Wei
>>>>
>>>> On Jun 5, 2012, at 11:43 PM, Dan Du wrote:
>>>>
>>>>> Hi Robert,
>>>>>
>>>>> I have been experiencing something else, possibly related to yours,
>>>>> on a 64bit ubuntu laptop with 6g of ram.
>>>>>
>>>>> As I recall, when bumping to Bioc 2.10, the Rsubread installation kind
>>>>> of ate all the memory, basically froze the system so I had to call it
>>>>> off, yet building it on the server side turned out fine. So I think I
>>>>> just accepted that the new version may be 'computationally heavy' thus
>>>>> not suitable for a normal pc, though I did not find any mentioning of
>>>>> this increased memory requirement in the NEWS file.
>>>>>
>>>>> So currently Rsubread stays at 1.4.4 on that pc, all subsequent
>>>> versions
>>>>> of Rsubread drain the memory in the same way when compiling
>>>> Rsubread.so.
>>>>>
>>>>> Now I think I can confirm this on a 32-bit opensuse box, it did
>>>>> successfully built, but when running the example code in the manual,
>>>>> same segfault happens.
>>>>>
>>>>>
>>>>>> library(Rsubread)
>>>>>> ref <- system.file("extdata","reference.fa",package="Rsubread")
>>>>>> path <- system.file("extdata",package="Rsubread")
>>>>>> buildindex(basename=file.path(path,"reference_index"),reference=ref)
>>>>>
>>>>> Building a base-space index.
>>>>> Size of memory used=3700 MB
>>>>> Base name of the built index
>>>>> = /home/opensuse/R-patched/library/Rsubread/extdata/reference_index
>>>>>
>>>>> *** caught segfault ***
>>>>> address 0xdf03ee80, cause 'memory not mapped'
>>>>>
>>>>> Traceback:
>>>>> 1: .C("R_buildindex_wrapper", argc = as.integer(n), argv =
>>>>> as.character(cmd), PACKAGE = "Rsubread")
>>>>> 2: buildindex(basename = file.path(path, "reference_index"), reference
>>>>> = ref)
>>>>>
>>>>>> sessionInfo()
>>>>> R version 2.15.0 Patched (2012-06-04 r59517)
>>>>> Platform: i686-pc-linux-gnu (32-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] Rsubread_1.6.3
>>>>>
>>>>>
>>>>> Regards,
>>>>> Dan
>>>>>
>>>>> On Tue, 2012-06-05 at 09:45 +0200, Robert Castelo wrote:
>>>>>> hi,
>>>>>>
>>>>>> the computer room at my university where we do practicals on R &
>>>> Bioconductor runs a 32bit linux distribution and when i tried to run
>>>> the latest version of the Rsubread package (1.6.3) it crashes when
>>>> calling the buildindex() function on a multifasta file with the yeast
>>>> genome. this does *not* happen under a 64bit linux distribution.
>>>>>>
>>>>>> i have verified that installing the version before (1.4.4) on the
>>>> current R 2.15 it also crashes (on the 32bit), but two versions
>>>> before, the 1.1.1, it does *not* and it works smoothly on this 32bit
>>>> linux distribution.
>>>>>>
>>>>>> i'm pasting below the output of using the 1.6.3 and 1.1.1 on R 2.15
>>>> where allChr.fa is the multifasta file with the yeast genome.
>>>>>>
>>>>>> so i can manage by now the problem by using the 1.1.1 version on R
>>>> 2.15 for my teaching but i wonder whether there would be some easy
>>>> solution for this, or even if it could be a symptom of something else
>>>> that the Rsubread developers should worry about. i know that using a
>>>> 32bit system nowadays is quite obsolete but this is what i got for
>>>> teaching :( and i would be happy to let my students play with the
>>>> latest version of Rsubread in the future.
>>>>>>
>>>>>>
>>>>>> thanks!!!
>>>>>> robert.
>>>>>>
>>>>>> ======================Rsubread 1.6.3 on R 2.15=======================
>>>>>>
>>>>>>> library(Rsubread)
>>>>>>> sessionInfo()
>>>>>> R version 2.15.0 (2012-03-30)
>>>>>> Platform: i686-pc-linux-gnu (32-bit)
>>>>>>
>>>>>> locale:
>>>>>> [1] LC_CTYPE=ca_ES.UTF-8 LC_NUMERIC=C
>>>>>> [3] LC_TIME=ca_ES.UTF-8 LC_COLLATE=ca_ES.UTF-8
>>>>>> [5] LC_MONETARY=ca_ES.UTF-8 LC_MESSAGES=ca_ES.UTF-8
>>>>>> [7] LC_PAPER=C LC_NAME=C
>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>>> [11] LC_MEASUREMENT=ca_ES.UTF-8 LC_IDENTIFICATION=C
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] Rsubread_1.6.3
>>>>>>
>>>>>>> buildindex(basename="subreadindex", reference="allChr.fa",
>>>> memory=2500)
>>>>>>
>>>>>> Building a base-space index.
>>>>>> Size of memory used=2500 MB
>>>>>> Base name of the built index = subreadindex
>>>>>>
>>>>>> *** caught segfault ***
>>>>>> address 0xdf670cc0, cause 'memory not mapped'
>>>>>>
>>>>>> Traceback:
>>>>>> 1: .C("R_buildindex_wrapper", argc = as.integer(n), argv =
>>>> as.character(cmd), PACKAGE = "Rsubread")
>>>>>> 2: buildindex(basename = "subreadindex", reference = "allChr.fa",
>>>> memory = 2500)
>>>>>>
>>>>>> Possible actions:
>>>>>> 1: abort (with core dump, if enabled)
>>>>>> 2: normal R exit
>>>>>> 3: exit R without saving workspace
>>>>>> 4: exit R saving workspace
>>>>>> Selection:
>>>>>>
>>>>>>
>>>>>> ======================Rsubread 1.1.1 on R 2.15=======================
>>>>>>
>>>>>>> library(Rsubread)
>>>>>>> buildindex(basename="subreadindex", reference="allChr.fa",
>>>> memory=2500)
>>>>>>
>>>>>> Building the index in the base space.
>>>>>> Size of memory requested=2500 MB
>>>>>> Index base name = subreadindex
>>>>>> INDEX ITEMS PER PARTITION = 275940352
>>>>>>
>>>>>> completed=40.88%; time used=1.7s; rate=2955.1k bps/s; total=12m bps
>>>> completed=81.76%; time used=2.4s; rate=4111.8k
>>>> bps/s; total=12m bps
>>>>>> All the chromosome files are processed.
>>>>>> | Dumping index
>>>> [===========================================================>]
>>>>>> Index subreadindex is successfully built.
>>>>>>> sessionInfo()
>>>>>> R version 2.15.0 (2012-03-30)
>>>>>> Platform: i686-pc-linux-gnu (32-bit)
>>>>>>
>>>>>> locale:
>>>>>> [1] LC_CTYPE=ca_ES.UTF-8 LC_NUMERIC=C
>>>>>> [3] LC_TIME=ca_ES.UTF-8 LC_COLLATE=ca_ES.UTF-8
>>>>>> [5] LC_MONETARY=ca_ES.UTF-8 LC_MESSAGES=ca_ES.UTF-8
>>>>>> [7] LC_PAPER=C LC_NAME=C
>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>>> [11] LC_MEASUREMENT=ca_ES.UTF-8 LC_IDENTIFICATION=C
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] Rsubread_1.1.1
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
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>>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
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>>>
>>
>>
>>
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