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Question: GEOquerry and virtualArray
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gravatar for Blumenberg, Miroslav
3.6 years ago by
Blumenberg, Miroslav30 wrote:
I tried to load GEOquerry and virtualArray but am getting the following error messages (even after re-loading latest versions of R and Bioconductor): Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 7031 != reported length 35878 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 7031 != reported length 35878 2: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 188067 != reported length 1145037 3: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 539927 != reported length 2836490 4: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 7031 != reported length 51601 5: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 193909 != reported length 320154 6: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 7: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' What am I doing wrong? My RankProd is working fine. Please help, Miki Blumenberg, NYU Med School. ------------------------------------------------------------ This email message, including any attachments, is for th...{{dropped:14}}
ADD COMMENTlink modified 3.6 years ago by James W. MacDonald45k • written 3.6 years ago by Blumenberg, Miroslav30
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gravatar for James W. MacDonald
3.6 years ago by
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James W. MacDonald45k wrote:
Hi Miroslav, On 4/8/2014 9:53 AM, Blumenberg, Miroslav wrote: > I tried to load GEOquerry and virtualArray but am getting the following error messages (even after re-loading latest versions of R and Bioconductor): > > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open the connection > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 7031 != reported length 35878 > 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' > > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 7031 != reported length 35878 > 2: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 188067 != reported length 1145037 > 3: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 539927 != reported length 2836490 > 4: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 7031 != reported length 51601 > 5: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 193909 != reported length 320154 > 6: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 7: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' It looks at the very least like your bitops package is broken, so I would re-install that. You also neglect to show what code you were running before you got these errors, so any further troubleshooting is difficult to do. You also neglected to include your sessionInfo(). Best, Jim > > What am I doing wrong? My RankProd is working fine. > Please help, > Miki Blumenberg, NYU Med School. > > > ------------------------------------------------------------ > This email message, including any attachments, is for th...{{dropped:14}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 3.6 years ago by James W. MacDonald45k
Sorry. I downloaded bitops (there wasn't one before); the command > library("bitops") is OK, no error messages, but GEOquerry download still does not work. I included the whole session with error messages here: R version 3.0.3 (2014-03-06) -- "Warm Puppy" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite("GEOquery") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.3. Installing package(s) 'GEOquery' also installing the dependency 'RCurl' trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/RCurl_1.95-4.1.zip' Content type 'application/zip' length 2836490 bytes (2.7 Mb) opened URL downloaded 528 Kb trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/con trib/3.0/GEOquery_2.28.0.zip' Content type 'application/zip' length 13721218 bytes (13.1 Mb) opened URL downloaded 13.1 Mb Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 541387 != reported length 2836490 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'RCurl/DESCRIPTION', probable reason 'No such file or directory' > --------------------------- Here's the sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] bitops_1.0-6 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] tools_3.0.3 Thanks for the help! Miki. _______________________________________________________________ Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: Tuesday, April 08, 2014 9:59 AM To: Blumenberg, Miroslav Cc: 'bioconductor at r-project.org' Subject: Re: [BioC] GEOquerry and virtualArray Hi Miroslav, On 4/8/2014 9:53 AM, Blumenberg, Miroslav wrote: > I tried to load GEOquerry and virtualArray but am getting the following error messages (even after re-loading latest versions of R and Bioconductor): > > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open the connection > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 7031 != reported length 35878 > 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip > file > 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' > > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 7031 != reported length 35878 > 2: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 188067 != reported length 1145037 > 3: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 539927 != reported length 2836490 > 4: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 7031 != reported length 51601 > 5: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 193909 != reported length 320154 > 6: In unzip(zipname, exdir = dest) : error 1 in extracting from zip > file > 7: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' It looks at the very least like your bitops package is broken, so I would re-install that. You also neglect to show what code you were running before you got these errors, so any further troubleshooting is difficult to do. You also neglected to include your sessionInfo(). Best, Jim > > What am I doing wrong? My RankProd is working fine. > Please help, > Miki Blumenberg, NYU Med School. > > > ------------------------------------------------------------ > This email message, including any attachments, is for > th...{{dropped:14}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================
ADD REPLYlink written 3.6 years ago by Blumenberg, Miroslav30
Hmm, weird. I don't have this problem: > biocLite("RCurl") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'RCurl' trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/RCurl_1.95-4.1.zip' Content type 'application/zip' length 2836490 bytes (2.7 Mb) opened URL downloaded 2.7 Mb package ?RCurl? successfully unpacked and MD5 sums checked > biocLite("GEOquery") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'GEOquery' trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/GE Oquery_2.28.0.zip' Content type 'application/zip' length 13721218 bytes (13.1 Mb) opened URL downloaded 13.1 Mb package ?GEOquery? successfully unpacked and MD5 sums checked And it looks like the big problem for you is RCurl, which is 2.7 Mb, and you are only getting 528 Kb. So try biocLite("RCurl") alone to see if you can get the package, then try GEOquery. Best, Jim On 4/8/2014 10:42 AM, Blumenberg, Miroslav wrote: > Sorry. > I downloaded bitops (there wasn't one before); the command > library("bitops") is OK, no error messages, but GEOquerry download still does not work. > I included the whole session with error messages here: > > > R version 3.0.3 (2014-03-06) -- "Warm Puppy" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: x86_64-w64-mingw32/x64 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help >> biocLite("GEOquery") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version > 3.0.3. > Installing package(s) 'GEOquery' > also installing the dependency 'RCurl' > > trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/RCurl_1.95-4.1.zip' > Content type 'application/zip' length 2836490 bytes (2.7 Mb) > opened URL > downloaded 528 Kb > > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/GEOquery_2.28.0.zip' > Content type 'application/zip' length 13721218 bytes (13.1 Mb) > opened URL > downloaded 13.1 Mb > > Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open the connection > In addition: Warning messages: > 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 541387 != reported length 2836490 > 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file > 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : > cannot open compressed file 'RCurl/DESCRIPTION', probable reason 'No such file or directory' > --------------------------- > > > Here's the sessionInfo(): >> sessionInfo() > R version 3.0.3 (2014-03-06) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > other attached packages: > [1] bitops_1.0-6 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] tools_3.0.3 > > > Thanks for the help! > Miki. > > > _______________________________________________________________ > > Original Message----- > From: James W. MacDonald [mailto:jmacdon at uw.edu] > Sent: Tuesday, April 08, 2014 9:59 AM > To: Blumenberg, Miroslav > Cc: 'bioconductor at r-project.org' > Subject: Re: [BioC] GEOquerry and virtualArray > > Hi Miroslav, > > > On 4/8/2014 9:53 AM, Blumenberg, Miroslav wrote: >> I tried to load GEOquerry and virtualArray but am getting the following error messages (even after re-loading latest versions of R and Bioconductor): >> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : >> cannot open the connection >> In addition: Warning messages: >> 1: In download.file(url, destfile, method, mode = "wb", ...) : >> downloaded length 7031 != reported length 35878 >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip >> file >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : >> cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' >> >> In addition: Warning messages: >> 1: In download.file(url, destfile, method, mode = "wb", ...) : >> downloaded length 7031 != reported length 35878 >> 2: In download.file(url, destfile, method, mode = "wb", ...) : >> downloaded length 188067 != reported length 1145037 >> 3: In download.file(url, destfile, method, mode = "wb", ...) : >> downloaded length 539927 != reported length 2836490 >> 4: In download.file(url, destfile, method, mode = "wb", ...) : >> downloaded length 7031 != reported length 51601 >> 5: In download.file(url, destfile, method, mode = "wb", ...) : >> downloaded length 193909 != reported length 320154 >> 6: In unzip(zipname, exdir = dest) : error 1 in extracting from zip >> file >> 7: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : >> cannot open compressed file 'bitops/DESCRIPTION', probable reason 'No such file or directory' > It looks at the very least like your bitops package is broken, so I would re-install that. You also neglect to show what code you were running before you got these errors, so any further troubleshooting is difficult to do. > > You also neglected to include your sessionInfo(). > > Best, > > Jim > >> What am I doing wrong? My RankProd is working fine. >> Please help, >> Miki Blumenberg, NYU Med School. >> >> >> ------------------------------------------------------------ >> This email message, including any attachments, is for >> th...{{dropped:14}} >> >> _______________________________________________ >> 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 > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > ------------------------------------------------------------ > This email message, including any attachments, is for ...{{dropped:12}}
ADD REPLYlink written 3.6 years ago by James W. MacDonald45k
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