[Bioc-devel] bumphunter package has unstated dependency on digest package?
Martin Morgan
mtmorgan at fredhutch.org
Sat Aug 8 02:06:46 CEST 2015
On 08/07/2015 04:31 PM, Dan Tenenbaum wrote:
>
>
> ----- 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.
>
I did
> remove.packages("digest")
Removing package from '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2'
(as 'lib' is unspecified)
> biocLite("bumphunter")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
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
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
* 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/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/bumphunter'
* restoring previous
'/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/bumphunter'
and then edited ~/.Rprofile to contain
trace(loadNamespace, quote(print(package)))
and tried again, leading to a lot of output ending in
...
[1] "stats"
Tracing loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) on entry
[1] "pkgmaker"
Tracing loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) on entry
[1] "codetools"
Tracing loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) on entry
[1] "digest"
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/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/bumphunter'
* restoring previous
'/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2/bumphunter'
I then walked up the stack, seeing which package depends on digest
> library(codetools)
> library(pkgmaker)
Loading required package: registry
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'digest'
Error: package or namespace load failed for 'pkgmaker'
but...
> packageDescription("pkgmaker")$Imports
[1] "methods, tools, codetools, digest, stringr, xtable, grDevices"
so it seems like digest should be installed with 'pkgmaker'
> biocLite("pkgmaker")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) 'pkgmaker'
also installing the dependency '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
trying URL 'http://cran.rstudio.com/src/contrib/pkgmaker_0.22.tar.gz'
Content type 'application/x-gzip' length 351479 bytes (343 KB)
==================================================
downloaded 343 KB
...
So I'd guess that you had previously removed (or maybe installed in a directory
that is not available in your current installation?) digest but not pkgmaker. R
decided that since pkgmaker was installed, its dependencies must be installed, too.
Martin
> 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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>>
>
> _______________________________________________
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