[Bioc-devel] bumphunter package has unstated dependency on digest package?

Sat Aug 8 02:57:33 CEST 2015

Ah, that makes sense. I was setting up R on a computer that hadn't been 
used in a while, and it had a bunch of packages installed in /usr/local, 
including an old version of BioC that was preventing an upgrade. So I 
removed the R site-packages directory in /usr/local and started over. 
Somehow digest must have been installed in /usr/local but not pkgmaker, 
so removing it broke the dependency chain. No idea how it got into that 
state, but problem solved.

On 8/7/15 5:06 PM, Martin Morgan wrote:
> 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]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>