Konsole output Hello, I was recently setting up the latest version of R & Bioc on a system, installing all packages from scratch, and I ran into an error while installing bumphunter. It failed to install because it couldn't load the "digest" package. After installing this package manually, bumphunter installed and loaded just fine. My session transcript appears below:
Konsole output $ lsb_release -a LSB Version: core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noar ch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch:core-4.1-amd64:core-4.1-noarch:cxx-3.0-am d64:cxx-3.0-noarch:cxx-3.1-amd64:cxx-3.1-noarch:cxx-3.2-amd64:cxx-3.2-noarch:cxx-4.0-amd64:cxx-4.0-noarch: cxx-4.1-amd64:cxx-4.1-noarch:desktop-3.1-amd64:desktop-3.1-noarch:desktop-3.2-amd64:desktop-3.2-noarch:des ktop-4.0-amd64:desktop-4.0-noarch:desktop-4.1-amd64:desktop-4.1-noarch:graphics-2.0-amd64:graphics-2.0-noa rch:graphics-3.0-amd64:graphics-3.0-noarch:graphics-3.1-amd64:graphics-3.1-noarch:graphics-3.2-amd64:graph ics-3.2-noarch:graphics-4.0-amd64:graphics-4.0-noarch:graphics-4.1-amd64:graphics-4.1-noarch:languages-3.2 -amd64:languages-3.2-noarch:languages-4.0-amd64:languages-4.0-noarch:languages-4.1-amd64:languages-4.1-noa rch:multimedia-3.2-amd64:multimedia-3.2-noarch:multimedia-4.0-amd64:multimedia-4.0-noarch:multimedia-4.1-a md64:multimedia-4.1-noarch:printing-3.2-amd64:printing-3.2-noarch:printing-4.0-amd64:printing-4.0-noarch:p rinting-4.1-amd64:printing-4.1-noarch:qt4-3.1-amd64:qt4-3.1-noarch:security-4.0-amd64:security-4.0-noarch: security-4.1-amd64:security-4.1-noarch Distributor ID: Ubuntu Description: Ubuntu 15.04 Release: 15.04 Codename: vivid $ R --vanilla R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 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 3.1 (BiocInstaller 1.18.4), ?biocLite for help > biocLite("bumphunter") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1. Installing package(s) ‘bumphunter’ trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/bumphunter_1.8.0.tar.gz' Content type 'application/x-gzip' length 2483454 bytes (2.4 MB) ================================================== downloaded 2.4 MB * installing *source* package ‘bumphunter’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called ‘digest’ ERROR: lazy loading failed for package ‘bumphunter’ * removing ‘/home/padma/R/x86_64-pc-linux-gnu-library/3.2/bumphunter’ * restoring previous ‘/home/padma/R/x86_64-pc-linux-gnu-library/3.2/bumphunter’ The downloaded source packages are in ‘/tmp/RtmpNmMWxf/downloaded_packages’ Old packages: 'bumphunter', 'cluster', 'codetools', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'spatial' n Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘bumphunter’ had non-zero exit status > biocLite("digest") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1. Installing package(s) ‘digest’ trying URL 'http://cran.rstudio.com/src/contrib/digest_0.6.8.tar.gz' Content type 'application/x-gzip' length 97985 bytes (95 KB) ================================================== downloaded 95 KB * installing *source* package ‘digest’ ... ** package ‘digest’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pmurhash.c -o pmurhash.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xxhash.c -o xxhash.o gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR installing to /home/padma/R/x86_64-pc-linux-gnu-library/3.2/digest/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (digest) The downloaded source packages are in ‘/tmp/RtmpNmMWxf/downloaded_packages’ Old packages: 'bumphunter', 'cluster', 'codetools', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'spatial' Update all/some/none? [a/s/n]: n > biocLite("bumphunter") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1. Installing package(s) ‘bumphunter’ trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/bumphunter_1.8.0.tar.gz' Content type 'application/x-gzip' length 2483454 bytes (2.4 MB) ================================================== downloaded 2.4 MB * installing *source* package ‘bumphunter’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ * DONE (bumphunter) The downloaded source packages are in ‘/tmp/RtmpNmMWxf/downloaded_packages’ Old packages: 'cluster', 'codetools', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'spatial' Update all/some/none? [a/s/n]: n > sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.04 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.18.4 loaded via a namespace (and not attached): [1] tools_3.2.1 Konsole output > library(bumphunter) Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: foreach foreach: simple, scalable parallel programming from Revolution Analytics Use Revolution R for scalability, fault tolerance and more. http://www.revolutionanalytics.com Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel