[Bioc-devel] bumphunter package has unstated dependency on digest package?
Ryan C. Thompson
rct at thompsonclan.org
Sat Aug 8 01:27:57 CEST 2015
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
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