[Bioc-devel] bumphunter package has unstated dependency on digest package?
Dan Tenenbaum
dtenenba at fredhutch.org
Sat Aug 8 01:31:31 CEST 2015
----- Original Message -----
> From: "Ryan C. Thompson" <rct at thompsonclan.org>
> To: bioc-devel at r-project.org
> Sent: Friday, August 7, 2015 4:27:57 PM
> Subject: [Bioc-devel] bumphunter package has unstated dependency on digest package?
>
> 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.
The string 'digest' does not occur in the bumphunter package (release version).
I wonder if it's another of bumphunter's dependencies that depends on digest and is not properly declaring that dependency.
Dan
> 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]]
>
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