Dear list, It seems that there is an issue with Rhtslib::pkgconfig() regarding the identification of the location of the shared library on some systems: https://support.bioconductor.org/p/102248/ To summarize: on this system, R is putting the shared library in lib64/, while pkgconfig() looks for it in lib/. This results in linkage errors for all packages depending on Rhtslib on this system. I imagine that the same would happen for all library packages, e.g., beachmat, Rhdf5lib. Looking at the Makevars for Rhtslib suggests that the shared library is stored in ${R_PACKAGE_DIR}/lib${R_ARCH}, while pkgconfig only ever looks in lib/. I assume that this usually works because ${R_ARCH} is empty on most linux systems, though perhaps this cannot be guaranteed. Cheers, Aaron
[Bioc-devel] possible bug in Rhtslib::pkgconfig
3 messages · Martin Morgan, Aaron Lun
Thanks Aaron I'll follow up on the support site. Can you clarify where the 'Re:' came from in the title? I can't find a previous post with similar title. Martin
On 10/27/2017 05:42 AM, Aaron Lun wrote:
Dear list, It seems that there is an issue with Rhtslib::pkgconfig() regarding the identification of the location of the shared library on some systems: https://support.bioconductor.org/p/102248/ To summarize: on this system, R is putting the shared library in lib64/, while pkgconfig() looks for it in lib/. This results in linkage errors for all packages depending on Rhtslib on this system. I imagine that the same would happen for all library packages, e.g., beachmat, Rhdf5lib. Looking at the Makevars for Rhtslib suggests that the shared library is stored in ${R_PACKAGE_DIR}/lib${R_ARCH}, while pkgconfig only ever looks in lib/. I assume that this usually works because ${R_ARCH} is empty on most linux systems, though perhaps this cannot be guaranteed. Cheers, Aaron
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The "Re:" in the title of this e-mail? I add an "Re:" to all my titles, and I assume that the mailing list dispatcher adds the "[Bioc-devel]" tag (cleverly inserting it between the "Re:" and the actual title). Just looked it up - apparently it stands for "in re" in Latin. I guess I learn something new every day.
Martin Morgan wrote:
Thanks Aaron I'll follow up on the support site. Can you clarify where the 'Re:' came from in the title? I can't find a previous post with similar title. Martin On 10/27/2017 05:42 AM, Aaron Lun wrote:
Dear list, It seems that there is an issue with Rhtslib::pkgconfig() regarding the identification of the location of the shared library on some systems: https://support.bioconductor.org/p/102248/ To summarize: on this system, R is putting the shared library in lib64/, while pkgconfig() looks for it in lib/. This results in linkage errors for all packages depending on Rhtslib on this system. I imagine that the same would happen for all library packages, e.g., beachmat, Rhdf5lib. Looking at the Makevars for Rhtslib suggests that the shared library is stored in ${R_PACKAGE_DIR}/lib${R_ARCH}, while pkgconfig only ever looks in lib/. I assume that this usually works because ${R_ARCH} is empty on most linux systems, though perhaps this cannot be guaranteed. Cheers, Aaron
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