Help installing 'rhdf5' in an "offline" environment
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Ole Rogeberg ▴ 20
@ole-rogeberg-6679
Last seen 7.2 years ago
I would like to install rhdf5 in a secured, Windows-based server environment that (for security reasons) cannot access outside servers or websites. As the environment is "offline" in this sense, I cannot use the recommended procedure involving biocLite.R and the bioconductor repository directly for installing the rhdf5 package. I can upload specific files to the offline environment, but not install software directly myself (lack write-access to the relevant folders on the server where software is located). However, the system administrator has placed a mirror of CRAN in the "offline" environment, and installing new CRAN packages in R is unproblematic. For rhdf5 I have tried: 1. Install rhdf5 directly: Uploading the rhdf5_2.8.0.tar.gz file and installing it from the package manager in RStudio. This gives the message that "ERROR: dependency 'zlibbioc' is not available for package 'rhdf5'" 2. Installing required packages that rhdf5 relies on: Uploading and installing zlibbioc in the same manner. This gives me a warning that "This package has a configure script. It probably needs manual configuration" - followed by a compilation error (see full R-message here <http: screencast.com="" t="" 2btxvwuz="">). I am unable to figure out what the "status 127" error message refers to, or if this is even a sensible way to proceed. Has anyone got a simple solution that I can implement or (if needed) a more technical solution I can forward to my system administrator? Sincerely, Ole Rogeberg [[alternative HTML version deleted]]
rhdf5 zlibbioc rhdf5 zlibbioc • 1.5k views
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@wolfgang-huber-3550
Last seen 7 days ago
EMBL European Molecular Biology Laborat…
Ole sounds like a challenging environment. Did you check the vignette of the zlibbioc package (available from http://www.bioconductor.org/packages/release/bioc/html/zlibbioc.html ) - perhaps you need to go into the configure file zlibbioc/src/zlib-1.2.5/configure and adapt. And/or, run the configure manually and see where it fails (it looks like the output you posted is truncated / missing important information). Wolfgang Il giorno Jul 30, 2014, alle ore 6:01 EDT, Ole Rogeberg <ole.rogeberg at="" gmail.com=""> ha scritto: > I would like to install rhdf5 in a secured, Windows-based server > environment that (for security reasons) cannot access outside servers or > websites. As the environment is "offline" in this sense, I cannot use the > recommended procedure involving biocLite.R and the bioconductor repository > directly for installing the rhdf5 package. > > I can upload specific files to the offline environment, but not install > software directly myself (lack write-access to the relevant folders on the > server where software is located). However, the system administrator has > placed a mirror of CRAN in the "offline" environment, and installing new > CRAN packages in R is unproblematic. > > For rhdf5 I have tried: > > 1. Install rhdf5 directly: Uploading the rhdf5_2.8.0.tar.gz file and > installing it from the package manager in RStudio. This gives the message > that "ERROR: dependency 'zlibbioc' is not available for package 'rhdf5'" > > 2. Installing required packages that rhdf5 relies on: Uploading and > installing zlibbioc in the same manner. This gives me a warning that "This > package has a configure script. It probably needs manual configuration" - > followed by a compilation error (see full R-message here > <http: screencast.com="" t="" 2btxvwuz="">). > > I am unable to figure out what the "status 127" error message refers to, or > if this is even a sensible way to proceed. > > Has anyone got a simple solution that I can implement or (if needed) a more > technical solution I can forward to my system administrator? > > Sincerely, > > Ole Rogeberg > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
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Dear Ole! Did you try to install the Windows binary package? zlibbioc_1.10.0.zip (32- & 64-bit) Bernd On 30.07.2014, at 14:05, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Ole > > sounds like a challenging environment. > Did you check the vignette of the zlibbioc package (available from http://www.bioconductor.org/packages/release/bioc/html/zlibbioc.html ) - perhaps you need to go into the configure file zlibbioc/src/zlib-1.2.5/configure and adapt. > And/or, run the configure manually and see where it fails (it looks like the output you posted is truncated / missing important information). > > Wolfgang > > > > > > > > Il giorno Jul 30, 2014, alle ore 6:01 EDT, Ole Rogeberg <ole.rogeberg at="" gmail.com=""> ha scritto: > >> I would like to install rhdf5 in a secured, Windows-based server >> environment that (for security reasons) cannot access outside servers or >> websites. As the environment is "offline" in this sense, I cannot use the >> recommended procedure involving biocLite.R and the bioconductor repository >> directly for installing the rhdf5 package. >> >> I can upload specific files to the offline environment, but not install >> software directly myself (lack write-access to the relevant folders on the >> server where software is located). However, the system administrator has >> placed a mirror of CRAN in the "offline" environment, and installing new >> CRAN packages in R is unproblematic. >> >> For rhdf5 I have tried: >> >> 1. Install rhdf5 directly: Uploading the rhdf5_2.8.0.tar.gz file and >> installing it from the package manager in RStudio. This gives the message >> that "ERROR: dependency 'zlibbioc' is not available for package 'rhdf5'" >> >> 2. Installing required packages that rhdf5 relies on: Uploading and >> installing zlibbioc in the same manner. This gives me a warning that "This >> package has a configure script. It probably needs manual configuration" - >> followed by a compilation error (see full R-message here >> <http: screencast.com="" t="" 2btxvwuz="">). >> >> I am unable to figure out what the "status 127" error message refers to, or >> if this is even a sensible way to proceed. >> >> Has anyone got a simple solution that I can implement or (if needed) a more >> technical solution I can forward to my system administrator? >> >> Sincerely, >> >> Ole Rogeberg >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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
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I had not tried the windows binary package - I had used the "package source". I tried the windows binary packages, and both zlibbioc and rhdf5 installed correctly! Thank you! Ole On Wed, Jul 30, 2014 at 8:52 PM, Bernd Fischer <bernd.fischer@embl.de> wrote: > Dear Ole! > > Did you try to install the Windows binary package? > zlibbioc_1.10.0.zip (32- & 64-bit) > > Bernd > On 30.07.2014, at 14:05, Wolfgang Huber <whuber@embl.de> wrote: > > > Ole > > > > sounds like a challenging environment. > > Did you check the vignette of the zlibbioc package (available from > http://www.bioconductor.org/packages/release/bioc/html/zlibbioc.html ) - > perhaps you need to go into the configure file > zlibbioc/src/zlib-1.2.5/configure and adapt. > > And/or, run the configure manually and see where it fails (it looks like > the output you posted is truncated / missing important information). > > > > Wolfgang > > > > > > > > > > > > > > > > Il giorno Jul 30, 2014, alle ore 6:01 EDT, Ole Rogeberg < > ole.rogeberg@gmail.com> ha scritto: > > > >> I would like to install rhdf5 in a secured, Windows-based server > >> environment that (for security reasons) cannot access outside servers or > >> websites. As the environment is "offline" in this sense, I cannot use > the > >> recommended procedure involving biocLite.R and the bioconductor > repository > >> directly for installing the rhdf5 package. > >> > >> I can upload specific files to the offline environment, but not install > >> software directly myself (lack write-access to the relevant folders on > the > >> server where software is located). However, the system administrator has > >> placed a mirror of CRAN in the "offline" environment, and installing new > >> CRAN packages in R is unproblematic. > >> > >> For rhdf5 I have tried: > >> > >> 1. Install rhdf5 directly: Uploading the rhdf5_2.8.0.tar.gz file and > >> installing it from the package manager in RStudio. This gives the > message > >> that "ERROR: dependency 'zlibbioc' is not available for package 'rhdf5'" > >> > >> 2. Installing required packages that rhdf5 relies on: Uploading and > >> installing zlibbioc in the same manner. This gives me a warning that > "This > >> package has a configure script. It probably needs manual configuration" > - > >> followed by a compilation error (see full R-message here > >> <http: screencast.com="" t="" 2btxvwuz="">). > >> > >> I am unable to figure out what the "status 127" error message refers > to, or > >> if this is even a sensible way to proceed. > >> > >> Has anyone got a simple solution that I can implement or (if needed) a > more > >> technical solution I can forward to my system administrator? > >> > >> Sincerely, > >> > >> Ole Rogeberg > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@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@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
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