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

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


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