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Question: Bioconductor SVN server error
0
gravatar for emathe
15 months ago by
emathe0
emathe0 wrote:

Hello,

I'm trying to have my package install with all of its CRAN and BioC dependencies. In an attempt to do so, I've installed the latest github:

> install_github("ewymathe/testALTREinstall")
Downloading GitHub repo ewymathe/testALTREinstall@master
from URL https://api.github.com/repos/ewymathe/testALTREinstall/zipball/master
Installing ALTRE
Error validating server certificate for 'https://hedgehog.fhcrc.org:443':
- The certificate is not issued by a trusted authority. Use the
   fingerprint to validate the certificate manually!
Certificate information:
- Hostname: *.fhcrc.org
- Valid: from Sat, 18 Oct 2014 16:52:00 GMT until Fri, 23 Nov 2018 15:15:23 GMT
- Issuer: http://certs.godaddy.com/repository/, GoDaddy.com, Inc., Scottsdale, Arizona, US
- Fingerprint: 55:64:9d:ce:78:a9:b0:b4:2f:df:4c:c6:59:b1:51:56:bb:5c:44:6a
(R)eject, accept (t)emporarily or accept (p)ermanently? t
svn: warning: W170000: URL 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/or.Hs.eg.db' non-existent in revision 120432

svn: E200009: Could not display info for all targets because some targets don't exist
Installation failed: There was a problem retrieving the current SVN revision
Warning message:
running command ''/usr/bin/svn' info --xml --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/or.Hs.eg.db' had status 1

Per the devtools' developers suggestion, I have run the following to accept the certificate permanently:

Ewys-MBP:~ ewymathe$ svn info https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks

Error validating server certificate for 'https://hedgehog.fhcrc.org:443':
 - The certificate is not issued by a trusted authority. Use the
   fingerprint to validate the certificate manually!
Certificate information:
 - Hostname: *.fhcrc.org
 - Valid: from Sat, 18 Oct 2014 16:52:00 GMT until Fri, 23 Nov 2018 15:15:23 GMT
 - Issuer: http://certs.godaddy.com/repository/, GoDaddy.com, Inc., Scottsdale, Arizona, US
 - Fingerprint: 55:64:9d:ce:78:a9:b0:b4:2f:df:4c:c6:59:b1:51:56:bb:5c:44:6a
(R)eject, accept (t)emporarily or accept (p)ermanently? p
Path: Rpacks
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks
Repository Root: https://hedgehog.fhcrc.org/bioconductor
Repository UUID: bc3139a8-67e5-0310-9ffc-ced21a209358
Revision: 120436
Node Kind: directory
Last Changed Author: jspidlen@bccrc.ca
Last Changed Rev: 120432
Last Changed Date: 2016-08-25 16:34:54 -0400 (Thu, 25 Aug 2016)

This however did not solve my problem.

Any fix for this?

ADD COMMENTlink modified 15 months ago • written 15 months ago by emathe0

Sorry, here is my sessionInfo():

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] devtools_1.12.0.9000

loaded via a namespace (and not attached):
[1] httr_1.2.1    R6_2.1.2      withr_1.0.2   curl_1.2      memoise_1.0.0
[6] git2r_0.15.0  digest_0.6.10

 

ADD REPLYlink written 15 months ago by emathe0
0
gravatar for Martin Morgan
15 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

This

https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/or.Hs.eg.db

points to an invalid location -- that should be 'org.Hs.eg.db', and these are not in the RELEASE_3_3 branch of svn, but rather available from the 'BioCann' repository of BiocInstaller::biocinstallRepos() at

https://bioconductor.org/packages/release/data/annotation

I would guess the problem is the incorrect use of Remotes: bioc::release/org.Hs.eg.db line. Ironically I think if this line were absent and one used BiocInstaller::biocLite("ewymathe/testALTREinstall") all would have been fine. Removing the remote and using biocLite() seems to be successful with the cloned and edited repository

biocLite("mtmorgan/testALTREinstall")
ADD COMMENTlink modified 15 months ago • written 15 months ago by Martin Morgan ♦♦ 20k
0
gravatar for emathe
15 months ago by
emathe0
emathe0 wrote:

Thanks for your prompt suggestion.  Unforunately, I am still getting a similar error:

> biocLite("mtmorgan/testALTREinstall")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing github package(s) ‘mtmorgan/testALTREinstall’
Downloading GitHub repo mtmorgan/testALTREinstall@master
from URL https://api.github.com/repos/mtmorgan/testALTREinstall/zipball/master
Installing ALTRE
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/j4/m74j380917j4njwrrvf2fh480000gn/T/Rtmp4wopXP/devtools35f57a02a09/mtmorgan-testALTREinstall-b1d333a'  \
  --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library'  \
  --install-tests

ERROR: dependency ‘org.Hs.eg.db’ is not available for package ‘ALTRE’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’
Installation failed: Command failed (1)

What's strange, is that for other Bioconductor packages (e.g. DESeq2), it automatically installs.  However, the following packages do not automatically install, including org.Hs.eg.db, ensDb.Hsapiens.v75, GO.db.

 

 

 

 

ADD COMMENTlink modified 15 months ago • written 15 months ago by emathe0

Your response is a 'COMMENT' rather than 'answer'. Maybe you have a setting options(pkgType=) that is different from the default ('both'), or the package org.Hs.eg.db is installed but in a location that is not seen by devtools? (I'm not sure how this would happen).  I guess a work-around is to install the packages independently biocLite("org.Hs.eg.db").

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 20k

I have tried setting options(pkgType="both") but to no avail.  As for org.Hs.eg.db, I have purposefully removed it from my machine to test this out.  Yes, the work-around you propose would work, but I do not want users to have to type many lines of code to install my package...

Could you explain what "non-existent in revision 120448" means?

ADD REPLYlink written 15 months ago by emathe0

Did you use remove.packages() to remove the package, and start a new R session? Maybe R thinks it still has org.* installed (use remove.packages() until R says there are no packages to remove, and confirm what R is telling your by checking that no directory in .libPaths() contains org.*. Also, while not relevant in this case, be careful with these types of operations. If pkg A depends on pkg B depends on pkg C, you remove pkg C and try to install pkg A, R will see that the immediate dependencies of pkg A are satisfied and will not install pkg C.

The "non-existent in revision 120448" is devtools trying to install the org.* from the Bioconductor SVN repository of package source code (rather than from the public repository of built packages). It is consulting the head of the SVN repository (revision 120448) and not finding org.*. It isn't found because, unlike Bioconductor software or experiment data packages, org packages are not in SVN.

You do not want your users to be installing from SVN, because then they require the full suite of compilation tools and supporting software libraries; it is much more appropriate to use the 'repos' argument of install_github (eventually, this argument is passed to install.packages) and set it to the correct repositories for the version of Bioconductor in use... BiocInstaller::biocinstallRepos(). This is what biocLite() does.

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 20k

Thanks for the explanation.

I have tried your suggestion but am still getting an error:

 

> install_github("ewymathe/testALTREinstall",repos=BiocInstaller::biocinstallRepos())
Downloading GitHub repo ewymathe/testALTREinstall@master
from URL https://api.github.com/repos/ewymathe/testALTREinstall/zipball/master
Installing ALTRE
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/j4/m74j380917j4njwrrvf2fh480000gn/T/Rtmp11dfFs/devtools74d75608b451/ewymathe-testALTREinstall-000280d'  \
  --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library'  \
  --install-tests

ERROR: dependency ‘org.Hs.eg.db’ is not available for package ‘ALTRE’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ALTRE’
Installation failed: Command failed (1)

 

where:

 

> BiocInstaller::biocinstallRepos()
                                               BioCsoft
           "https://bioconductor.org/packages/3.3/bioc"
                                                BioCann
"https://bioconductor.org/packages/3.3/data/annotation"
                                                BioCexp
"https://bioconductor.org/packages/3.3/data/experiment"
                                              BioCextra
          "https://bioconductor.org/packages/3.3/extra"
                                                   CRAN
                             "https://cran.rstudio.com"

 

ADD REPLYlink written 14 months ago by emathe0

It is not a problem that I can reproduce, so cannot help you further. Maybe someone else on the list has something to say.

ADD REPLYlink written 14 months ago by Martin Morgan ♦♦ 20k
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