Re: [gentoo-user] Doubt about R support in gentoo
Yeah, thank you. ICU is a great pain in the ring! Regards On 11/19/2016 12:26 PM, c0a80...@gmail.com wrote: On 11/19/16 12:50, Alec Ten Harmsel wrote: El 19/11/2016 a las 07:47 a. m., Zhu Sha Zang escribió: Hello everybody... A single doubt here: After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i tried a package upgrade inside R and got that: /> update.packages(checkBuilt=TRUE, ask=FALSE, repos='http://cran.us.r-project.org') trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz' Content type 'application/x-gzip' length 1027358 bytes (1003 KB) == downloaded 1003 KB * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : *unable to load shared object '/usr/lib64/R/library/stringi/libs/stringi.so':** ** libicui18n.so.57: cannot open shared object file: No such file or directory* / I am not super familiar with R - can you try rebuilding R itself before doing the CRAN package installs/upgrades? It looks like the path to ICU is hard-coded somehow. This kind of "bug" can I put inside bugs.gentoo.org or its a cran package bug? It is not the first time and i'm in dout about how to proceed. If rebuildling R fixes this problem, you can file a bug so that developers somehow trigger an R rebuild whenever ICU is updated. Alec Some R package update errors may be solved by creating a temporary folder, for example ~/R/tmp (placing it under ~/R has the advantage of sharing the same parent directory as the default per-user package library), and then passing the following environment variable to R: TMPDIR=$HOME/R/tmp. This allows certain configure scripts to be executed if your /tmp is mounted noexec. As for the stringi error, my system doesn't have it in the system-wide library, either: $ ls /usr/lib64/R/library/ KernSmooth compilermgcvstats4 MASSdatasetsnlmesurvival Matrix foreign nnettcltk basegrDevices paralleltools bootgraphicsrpart translations class gridspatial utils cluster lattice splines codetools methods stats But: $ ls ~/R/x86_64-pc-linux-gnu-library/3.2/stringi AUTHORS LICENSE R libs CITATIONMetahelp DESCRIPTION NAMESPACE html INDEX NEWSinclude Another possibility may be that your R has a useflag for icu (mine doesn't): $ equery uses R [ Legend : U - final flag setting for installation] [: I - package is installed with flag ] [ Colors : set, unset ] * Found these USE flags for dev-lang/R-3.2.2: U I ... + + doc : Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally - - icu : Enable ICU (Internationalization Components for Unicode) support, using dev-libs/icu - - java: Add support for Java ... Vitor
Re: [gentoo-user] Doubt about R support in gentoo
On 11/19/16 12:50, Alec Ten Harmsel wrote: El 19/11/2016 a las 07:47 a. m., Zhu Sha Zang escribió: Hello everybody... A single doubt here: After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i tried a package upgrade inside R and got that: /> update.packages(checkBuilt=TRUE, ask=FALSE, repos='http://cran.us.r-project.org') trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz' Content type 'application/x-gzip' length 1027358 bytes (1003 KB) == downloaded 1003 KB * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : *unable to load shared object '/usr/lib64/R/library/stringi/libs/stringi.so':** ** libicui18n.so.57: cannot open shared object file: No such file or directory* / I am not super familiar with R - can you try rebuilding R itself before doing the CRAN package installs/upgrades? It looks like the path to ICU is hard-coded somehow. This kind of "bug" can I put inside bugs.gentoo.org or its a cran package bug? It is not the first time and i'm in dout about how to proceed. If rebuildling R fixes this problem, you can file a bug so that developers somehow trigger an R rebuild whenever ICU is updated. Alec Some R package update errors may be solved by creating a temporary folder, for example ~/R/tmp (placing it under ~/R has the advantage of sharing the same parent directory as the default per-user package library), and then passing the following environment variable to R: TMPDIR=$HOME/R/tmp. This allows certain configure scripts to be executed if your /tmp is mounted noexec. As for the stringi error, my system doesn't have it in the system-wide library, either: $ ls /usr/lib64/R/library/ KernSmooth compilermgcvstats4 MASSdatasetsnlmesurvival Matrix foreign nnettcltk basegrDevices paralleltools bootgraphicsrpart translations class gridspatial utils cluster lattice splines codetools methods stats But: $ ls ~/R/x86_64-pc-linux-gnu-library/3.2/stringi AUTHORS LICENSE R libs CITATIONMetahelp DESCRIPTION NAMESPACE html INDEX NEWSinclude Another possibility may be that your R has a useflag for icu (mine doesn't): $ equery uses R [ Legend : U - final flag setting for installation] [: I - package is installed with flag ] [ Colors : set, unset ] * Found these USE flags for dev-lang/R-3.2.2: U I ... + + doc : Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally - - icu : Enable ICU (Internationalization Components for Unicode) support, using dev-libs/icu - - java: Add support for Java ... Vitor
Re: [gentoo-user] Doubt about R support in gentoo
El 19/11/2016 a las 07:47 a. m., Zhu Sha Zang escribió: Hello everybody... A single doubt here: After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i tried a package upgrade inside R and got that: /> update.packages(checkBuilt=TRUE, ask=FALSE, repos='http://cran.us.r-project.org') trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz' Content type 'application/x-gzip' length 1027358 bytes (1003 KB) == downloaded 1003 KB * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : *unable to load shared object '/usr/lib64/R/library/stringi/libs/stringi.so':** ** libicui18n.so.57: cannot open shared object file: No such file or directory* / I am not super familiar with R - can you try rebuilding R itself before doing the CRAN package installs/upgrades? It looks like the path to ICU is hard-coded somehow. This kind of "bug" can I put inside bugs.gentoo.org or its a cran package bug? It is not the first time and i'm in dout about how to proceed. If rebuildling R fixes this problem, you can file a bug so that developers somehow trigger an R rebuild whenever ICU is updated. Alec
[gentoo-user] Doubt about R support in gentoo
Hello everybody... A single doubt here: After an upgrade in package dev-libs/icu (from 57.1 to 58.1-r1) i tried a package upgrade inside R and got that: /> update.packages(checkBuilt=TRUE, ask=FALSE, repos='http://cran.us.r-project.org') trying URL 'http://cran.us.r-project.org/src/contrib/knitr_1.15.tar.gz' Content type 'application/x-gzip' length 1027358 bytes (1003 KB) == downloaded 1003 KB * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : *unable to load shared object '/usr/lib64/R/library/stringi/libs/stringi.so':** ** libicui18n.so.57: cannot open shared object file: No such file or directory* Error : unable to load R code in package ‘knitr’ ERROR: lazy loading failed for package ‘knitr’ * removing ‘/usr/lib64/R/library/knitr’ * restoring previous ‘/usr/lib64/R/library/knitr’ The downloaded source packages are in ‘/tmp/RtmpKBphr0/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘knitr’ had non-zero exit status / This kind of "bug" can I put inside bugs.gentoo.org or its a cran package bug? It is not the first time and i'm in dout about how to proceed. Thanks anyway. Best regards!! //
