Dear Dan, Thanks for letting us know. That's great! Cheers, Wei On Jun 8, 2012, at 4:09 PM, Dan Du wrote: > Dear Wei, > > Good work, memory freed. Just checkout the devel version, package built > and installed successfully with no hiccup, test codes runs fine. > > Regards, > Dan > > On Fri, 2012-06-08 at 12:10 +1000, Wei Shi wrote: >> Dear Robert, Dan and Peter, >> >> We have made changes to a number of functions in the package to reduce the memory allocated to Rsubread by the operating system when it was loaded. The new version has been committed to both bioc release (Rsubread 1.6.4) and bioc devel (Rsubread 1.7.4). They should be available to you in a day or two. >> >> Also, the buildindex() function no longer needs the allocation of 1GB continuous memory region. But it will still consume at least 1GB of memory when it is running, no matter what the given value of the 'memory' parameter is. >> >> We have tested the new version on our 32-bit VM machine (it has 3GB of memory and the value of 'memory' parameter used by buildindex was 2500) and it solves all the reported problems, so we are pretty happy with it. I hope the new version works in your computers/laptops, but please do let us know if it doesn't. >> >> Sorry about the problems you have encountered. It's always a challenge to develop a R package with so much C code in it! >> >> Cheers, >> 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/Rsubre ad_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 >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>>> ______________________________________________________________________ >>>>>> The information in this email is confidential and intended solely for >>>>>> the addressee. >>>>>> You must not disclose, forward, print or use it without the permission >>>>>> of the sender. >>>>>> ______________________________________________________________________ >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> ______________________________________________________________________ >>>> The information in this email is confidential and intended solely for the addressee. >>>> You must not disclose, forward, print or use it without the permission of the sender. >>>> ______________________________________________________________________ >>> >>> >> >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the addressee. >> You must not disclose, forward, print or use it without the permission of the sender. >> ______________________________________________________________________ > > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}

Dear Robert, That's great. Thanks for letting us know. Cheers, Wei > Dear Wei, > > it also works on my side, the 32 bit machines do not crash anymore. > > thanks for solving this so quickly! > robert. > > On 06/08/2012 04:10 AM, Wei Shi wrote: >> Dear Robert, Dan and Peter, >> >> We have made changes to a number of functions in the package to reduce >> the memory allocated to Rsubread by the operating system when it was >> loaded. The new version has been committed to both bioc release >> (Rsubread 1.6.4) and bioc devel (Rsubread 1.7.4). They should be >> available to you in a day or two. >> >> Also, the buildindex() function no longer needs the allocation of 1GB >> continuous memory region. But it will still consume at least 1GB of >> memory when it is running, no matter what the given value of the >> 'memory' parameter is. >> >> We have tested the new version on our 32-bit VM machine (it has 3GB of >> memory and the value of 'memory' parameter used by buildindex was 2500) >> and it solves all the reported problems, so we are pretty happy with it. >> I hope the new version works in your computers/laptops, but please do >> let us know if it doesn't. >> >> Sorry about the problems you have encountered. It's always a challenge >> to develop a R package with so much C code in it! >> >> Cheers, >> 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/Rsubre ad_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 >> ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}