Is it just me, or did a corrupt PACKAGES.gz file get installed in the bin/windows/contrib/3.2 directory of CRAN mirrors recently? gzfile() complains about it and Cygwin's gzip cannot decompress it. I tried the following repos <- "https://cran.rstudio.com" v <- "3.2" pkgs.gz <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES.gz") tfile <- tempfile(fileext=".gz") download.file(pkgs.gz, dest=tfile) r.gz <- readLines(gzfile(tfile, "r")) tail(system(paste("c:\\cygwin\\bin\\gzip -d - ", shQuote(tfile)), intern=TRUE)) and got> repos <- "https://cran.rstudio.com" > v <- "3.2" > pkgs.gz <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES.gz") > > tfile <- tempfile(fileext=".gz") > download.file(pkgs.gz, dest=tfile)trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/PACKAGES.gz' Content type 'application/x-gzip' length 188174 bytes (183 KB) downloaded 183 KB> r.gz <- readLines(gzfile(tfile, "r"))Warning message: In readLines(gzfile(tfile, "r")) : seek on a gzfile connection returned an internal error> tail(system(paste("c:\\cygwin\\bin\\gzip -d - ", shQuote(tfile)),intern=TRUE)) [1] "" "gzip: stdin: unexpected end of file" Warning message: running command 'c:\cygwin\bin\gzip -d - "C:\Users\wdunlap\AppData\Local\Temp\RtmpG42jk4\file2a201a9e4802.gz"' had status 1 R's gz code seems to recover from the bad seek, but Cygwin's gzip cannot.> pkgs <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES") > r <- readLines(url(pkgs, "rt")) > all.equal(r, r.gz)[1] TRUE I get the same results using the Spanish miror, https://ftp.cixug.es/CRAN Bill Dunlap TIBCO Software wdunlap tibco.com [[alternative HTML version deleted]]
Bill, thanks for reporting, this is currently true for all PACKAGES.gz files my autobuilder is creating, will investigate. Best, Uwe On 06.11.2015 18:54, William Dunlap wrote:> Is it just me, or did a corrupt PACKAGES.gz file get installed in the > bin/windows/contrib/3.2 directory of CRAN mirrors recently? gzfile() > complains about it and Cygwin's gzip cannot decompress it. I tried the > following > > repos <- "https://cran.rstudio.com" > v <- "3.2" > pkgs.gz <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES.gz") > > tfile <- tempfile(fileext=".gz") > download.file(pkgs.gz, dest=tfile) > r.gz <- readLines(gzfile(tfile, "r")) > tail(system(paste("c:\\cygwin\\bin\\gzip -d - ", shQuote(tfile)), > intern=TRUE)) > > and got > >> repos <- "https://cran.rstudio.com" >> v <- "3.2" >> pkgs.gz <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES.gz") >> >> tfile <- tempfile(fileext=".gz") >> download.file(pkgs.gz, dest=tfile) > trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/PACKAGES.gz' > Content type 'application/x-gzip' length 188174 bytes (183 KB) > downloaded 183 KB > >> r.gz <- readLines(gzfile(tfile, "r")) > Warning message: > In readLines(gzfile(tfile, "r")) : > seek on a gzfile connection returned an internal error >> tail(system(paste("c:\\cygwin\\bin\\gzip -d - ", shQuote(tfile)), > intern=TRUE)) > [1] "" "gzip: stdin: unexpected end of > file" > Warning message: > running command 'c:\cygwin\bin\gzip -d - > "C:\Users\wdunlap\AppData\Local\Temp\RtmpG42jk4\file2a201a9e4802.gz"' had > status 1 > > R's gz code seems to recover from the bad seek, but Cygwin's gzip cannot. > >> pkgs <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES") >> r <- readLines(url(pkgs, "rt")) >> all.equal(r, r.gz) > [1] TRUE > > I get the same results using the Spanish miror, https://ftp.cixug.es/CRAN > > > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
My test may not have been entirely right, but it looks like the PACKAGES.gz file for windows binary packages for R-3.2.x was a quarter of its usual size on Nov 5-6, 2015. It is now fine. I used Revolution's daily CRAN snapshots to check. mran.revolutionanalytics.com/snapshot/YYYY-MM-DD Bill Dunlap TIBCO Software wdunlap tibco.com On Sat, Nov 7, 2015 at 12:24 AM, Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote:> Bill, > > thanks for reporting, this is currently true for all PACKAGES.gz files my > autobuilder is creating, will investigate. > > Best, > Uwe > > > > On 06.11.2015 18:54, William Dunlap wrote: > >> Is it just me, or did a corrupt PACKAGES.gz file get installed in the >> bin/windows/contrib/3.2 directory of CRAN mirrors recently? gzfile() >> complains about it and Cygwin's gzip cannot decompress it. I tried the >> following >> >> repos <- "https://cran.rstudio.com" >> v <- "3.2" >> pkgs.gz <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES.gz") >> >> tfile <- tempfile(fileext=".gz") >> download.file(pkgs.gz, dest=tfile) >> r.gz <- readLines(gzfile(tfile, "r")) >> tail(system(paste("c:\\cygwin\\bin\\gzip -d - ", shQuote(tfile)), >> intern=TRUE)) >> >> and got >> >> repos <- "https://cran.rstudio.com" >>> v <- "3.2" >>> pkgs.gz <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES.gz") >>> >>> tfile <- tempfile(fileext=".gz") >>> download.file(pkgs.gz, dest=tfile) >>> >> trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/PACKAGES.gz' >> Content type 'application/x-gzip' length 188174 bytes (183 KB) >> downloaded 183 KB >> >> r.gz <- readLines(gzfile(tfile, "r")) >>> >> Warning message: >> In readLines(gzfile(tfile, "r")) : >> seek on a gzfile connection returned an internal error >> >>> tail(system(paste("c:\\cygwin\\bin\\gzip -d - ", shQuote(tfile)), >>> >> intern=TRUE)) >> [1] "" "gzip: stdin: unexpected end of >> file" >> Warning message: >> running command 'c:\cygwin\bin\gzip -d - >> "C:\Users\wdunlap\AppData\Local\Temp\RtmpG42jk4\file2a201a9e4802.gz"' >> had >> status 1 >> >> R's gz code seems to recover from the bad seek, but Cygwin's gzip cannot. >> >> pkgs <- paste(sep="/", repos, "bin/windows/contrib", v, "PACKAGES") >>> r <- readLines(url(pkgs, "rt")) >>> all.equal(r, r.gz) >>> >> [1] TRUE >> >> I get the same results using the Spanish miror, https://ftp.cixug.es/CRAN >> >> >> Bill Dunlap >> TIBCO Software >> wdunlap tibco.com >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >>[[alternative HTML version deleted]]