Errors installing Rcpp using R_Overlay

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Errors installing Rcpp using R_Overlay

Neil Shephard
Hi,

Delighted to discover the R_Overlay that allows package installation from CRAN under portage after a posting by maintainer Benda Xu a few weeks ago (http://gentoo.2317880.n4.nabble.com/Re-new-eclass-to-install-R-modules-such-as-Rcpp-td331686.html).

Found the time to sit down and start migrating/installing packages via the overlay and decided to start by installing the tidyverse package as it would pull in a host of dependencies and keep /var/lib/portage/world a bit smaller (it pulls in 60 packages in total).

Unfortunately Rcpp fails to build and so the vast majority (n = 56) pulled in when emerge tidyverse fail to install.

The build log is...

# cat /var/tmp/portage/sci-CRAN/Rcpp-0.12.15/temp/build.log
 * Package:    sci-CRAN/Rcpp-0.12.15
 * Repository: R_Overlay
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
x86_64-pc-linux-gnu-g++  -I/usr/lib64/R/include -DNDEBUG -I../inst/include/     -fpic  -march=skylake -O2 -pipe -c Date.cpp -o Date.o
x86_64-pc-linux-gnu-g++  -I/usr/lib64/R/include -DNDEBUG -I../inst/include/     -fpic  -march=skylake -O2 -pipe -c Module.cpp -o Module.o
x86_64-pc-linux-gnu-g++  -I/usr/lib64/R/include -DNDEBUG -I../inst/include/     -fpic  -march=skylake -O2 -pipe -c Rcpp_init.cpp -o Rcpp_init.o
x86_64-pc-linux-gnu-g++  -I/usr/lib64/R/include -DNDEBUG -I../inst/include/     -fpic  -march=skylake -O2 -pipe -c api.cpp -o api.o
x86_64-pc-linux-gnu-g++  -I/usr/lib64/R/include -DNDEBUG -I../inst/include/     -fpic  -march=skylake -O2 -pipe -c attributes.cpp -o attributes.o
x86_64-pc-linux-gnu-g++  -I/usr/lib64/R/include -DNDEBUG -I../inst/include/     -fpic  -march=skylake -O2 -pipe -c barrier.cpp -o barrier.o
x86_64-pc-linux-gnu-g++ -shared -L/usr/lib64/R/lib -Wl,-O1 -Wl,--as-needed -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib64/R/lib -lR
installing to /var/tmp/portage/sci-CRAN/Rcpp-0.12.15/work/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
Traceback (most recent call last):
  File "/usr/lib/portage/python3.5/doins.py", line 611, in <module>
    sys.exit(main(sys.argv[1:]))
  File "/usr/lib/portage/python3.5/doins.py", line 602, in main
    os.path.dirname(source)):
  File "/usr/lib/portage/python3.5/doins.py", line 450, in _doins
    return install_runner.install_file(source, os.path.dirname(dest))
  File "/usr/lib/portage/python3.5/doins.py", line 386, in install_file
    return self._ins_runner.run(source, dest_dir)
  File "/usr/lib/portage/python3.5/doins.py", line 195, in run
    sstat = os.stat(source)
FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/Rcpp-0.12.15/work/Rcppy'
 * ERROR: sci-CRAN/Rcpp-0.12.15::R_Overlay failed (install phase):
 *   doins failed
 * 
 * If you need support, post the output of `emerge --info '=sci-CRAN/Rcpp-0.12.15::R_Overlay'`,
 * the complete build log and the output of `emerge -pqv '=sci-CRAN/Rcpp-0.12.15::R_Overlay'`.
 * The complete build log is located at '/var/tmp/portage/sci-CRAN/Rcpp-0.12.15/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-CRAN/Rcpp-0.12.15/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-CRAN/Rcpp-0.12.15/work/Rcpp-0.12.15'
 * S: '/var/tmp/portage/sci-CRAN/Rcpp-0.12.15/work/Rcpp-0.12.15'


And I've placed the other information on pastebin...

#  emerge --info '=sci-CRAN/Rcpp-0.12.15::R_Overlay' | pastebinit

#  emerge -pqv '=sci-CRAN/Rcpp-0.12.15::R_Overlay' | pastebinit


Any thoughts on how to solve this?  It looks like Rcpp builds ok within R and the error arises when control is passed back to Portage.

I figured [hidden email] would be appropriate given Benda's recent post but apologies if this is not the case.


Neil

--
Natural selection is a mechanism for generating an exceedingly high degree of improbability. - R.A. Fisher


-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: Mailvelope 0.11.0
Comment: Email security by Mailvelope - https://www.mailvelope.com
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=9T81
-----END PGP PUBLIC KEY BLOCK-----

Reply | Threaded
Open this post in threaded view
|

Re: Errors installing Rcpp using R_Overlay

Benda Xu
Hi Neil,

I am sorry.  This bug was from my typographical error in the
R-packages.eclass.

Neil Shephard <[hidden email]> writes:

> FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/Rcpp-0.12.15/work/Rcppy'

There has been an extra "y" at the end of the line.

I am really sorry for the inconvenience caused.

> Any thoughts on how to solve this? It looks like Rcpp builds ok within
> R and the error arises when control is passed back to Portage.

Please rsync again and emerge Rcpp.

Cheers,
Benda

Reply | Threaded
Open this post in threaded view
|

Re: Errors installing Rcpp using R_Overlay

Neil Shephard
Hi Benda,

[Sending this to gentoo-science mailing list as accidentally replied direct, have also discovered a few other packages that have incorrect versions]

Hi Benda,

Thanks for taking the time to resolve this, that has worked nicely and Rcpp now emerges.

I continued trying to replace all the packages I have installed directly through R with emerges from R_Overlay and opted to emerge the meta-package tidyverse which pulls in a ton of packages as well as more explicit packages that aren't pulled in.  In doing so I've encountered three problems....


1. Some ebuilds try to pull in old versions.
2. Some ebuilds from R_Overlay require "USE=minimal dev-lang/R" whilst others require "USE=-minimal dev-lang/R" which makes it difficult to emerge things.
3. I found one package that is on CRAN but for which there is no ebuild.



1. Old Versions
============

I found the following old version were pulled in....

| Package   | R_Overlay Version | CRAN version  |
|-----------|-------------------|---------------|
| xml2      | 0.1.2             | 1.2.0         |
| lubridate | 1.7.0             | 1.7.3         |



2. dev-lang/R [-]minimal conflicts
==========================

Tried emerging a bundle of packages and get conflicts relating to the USE=minimal, also resulted in some slot conflicts that I couldn't see.  Its mostly the 'virtual/[pkg]' that require -minimal....

emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm lme4 glmnet rpart caret survival Hmisc rms epitools pwr TrialSize longpower simglm clusterPower samplesize PowerTOST blockrand bookdown
...

!!! Multiple package instances within a single package slot have been pulled
!!! into the dependency graph, resulting in a slot conflict:

dev-lang/R:0

  (dev-lang/R-3.4.4:0/0::slack, installed) pulled in by
    dev-lang/R[-minimal] required by (virtual/cluster-0:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^^                                                                                                                
    dev-lang/R[-minimal] required by (virtual/KernSmooth-0:0/0::R_Overlay, installed)
               ^^^^^^^^                                                                                                  
    dev-lang/R[-minimal] required by (virtual/MASS-0:0/0::R_Overlay, installed)
               ^^^^^^^^                                                                                            
    dev-lang/R[-minimal] required by (virtual/Matrix-0:0/0::R_Overlay, installed)
               ^^^^^^^^                                                                                              
    dev-lang/R[-minimal] required by (virtual/codetools-0:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^^                                                                                                                  
    dev-lang/R[-minimal] required by (virtual/class-0:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^^                                                                                                              
    dev-lang/R[-minimal] required by (virtual/foreign-0:0/0::R_Overlay, installed)
               ^^^^^^^^                                                                                               
    dev-lang/R[-minimal] required by (virtual/lattice-0:0/0::R_Overlay, installed)
               ^^^^^^^^                                                                                               
    dev-lang/R[-minimal] required by (virtual/nlme-0:0/0::R_Overlay, installed)
               ^^^^^^^^                                                                                            
    dev-lang/R[-minimal] required by (virtual/survival-0:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^^                                                                                                                 
    dev-lang/R[-minimal] required by (virtual/rpart-0:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^^                                                                                                              
    dev-lang/R[-minimal] required by (virtual/nnet-0:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^^                                                                                                             

  (dev-lang/R-3.4.4:0/0::slack, ebuild scheduled for merge) pulled in by
    dev-lang/R[minimal] required by (sci-CRAN/Matrix-1.2.12:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^                                                                                                                     
    dev-lang/R[minimal] required by (sci-CRAN/nlme-3.1.131.1:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^                                                                                                                      
    dev-lang/R[minimal] required by (sci-CRAN/rpart-4.1.13:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^                                                                                                                    
    dev-lang/R[minimal] required by (sci-CRAN/survival-2.41.3:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^                                                                                                                       
    dev-lang/R[minimal] required by (sci-CRAN/lattice-0.20.35:0/0::R_Overlay, ebuild scheduled for merge)
               ^^^^^^^                                                                                                                       



The following USE changes are necessary to proceed:
 (see "package.use" in the portage(5) man page for more details)
# required by sci-CRAN/survival-2.41.3::R_Overlay
# required by sci-CRAN/multcomp-1.4.8::R_Overlay
# required by sci-CRAN/rms-5.1.2::R_Overlay
# required by rms (argument)
>=dev-lang/R-3.4.4 minimal


Strangely virtual/rpart is listed as requiring USE=-minimal but the rpart package itself requires USE=minimal.


3. Missing ebuild for one package
==========================

I was going to try emergeing the blogdown package (https://cran.r-project.org/web/packages/blogdown/) but there is no ebuild for it in R_Overlay...

# emerge -av blogdown

emerge: there are no ebuilds to satisfy "blogdown".

emerge: searching for similar names...
emerge: Maybe you meant any of these: sci-CRAN/bookdown, sci-BIOC/ballgown, app-admin/logmon?




One minor caeveat is that I'm using a locally bumped version of R as the bugreport I've filed for bumping in portage (https://bugs.gentoo.org/632364) hasn't been addressed yet.  I'm currently using =dev-lang/R-3.4.4

I'm unsure how the ebuilds in R_Overlay are generated, is it automatically based on available builds?

Thanks for yours and others work on this, having R packages managed by portage is a real boon, as it removes the need to update.packages(ask = FALSE) so regularly.

If there is something I can do to help please let me know.

Neil


--
Natural selection is a mechanism for generating an exceedingly high degree of improbability. - R.A. Fisher

Ignorance more frequently begets confidence than does knowledge - by Charles Darwin

PGP Public : https://pgp.mit.edu/pks/lookup?op=get&search=0x0E7ECE9C10D7B4A0

Website - http://kimura.no-ip.info/
Photos - http://www.flickr.com/photos/slackline/


Reply | Threaded
Open this post in threaded view
|

Re: Errors installing Rcpp using R_Overlay

Benda Xu
Hi Neil,

Thank you!

Neil Shephard <[hidden email]> writes:

> Thanks for taking the time to resolve this, that has worked nicely and
> Rcpp now emerges.
>
> I continued trying to replace all the packages I have installed
> directly through R with emerges from R_Overlay and opted to emerge the
> meta-package tidyverse which pulls in a ton of packages as well as
> more explicit packages that aren't pulled in. In doing so I've
> encountered three problems....
>
> 1. Some ebuilds try to pull in old versions.

> 2. Some ebuilds from R_Overlay require "USE=minimal dev-lang/R" whilst
> others require "USE=-minimal dev-lang/R" which makes it difficult to
> emerge things.

> 3. I found one package that is on CRAN but for which there is no ebuild.
>
> 1. Old Versions
> ============
>
> I found the following old version were pulled in....
>
> | Package | R_Overlay Version | CRAN version |
> |-----------|-------------------|---------------|
> | xml2 | 0.1.2 | 1.2.0 |
> | lubridate | 1.7.0 | 1.7.3 |

This is because the parser fails on the new version.  Taking xml2 for
example, the "system requirements" field on CRAN is:

  libxml2: libxml2-dev (deb), libxml2-devel (rpm)

The parser did not know "(deb)" this maps to dev-libs/libxml2, nor it
could match 'libxml2-devel'.


Before I had to fix these cornor cases manually.  I am thinking of
exposing the configuration file so that users can contribute to the new
parsing rules.

> 2. dev-lang/R [-]minimal conflicts
> ==========================
>
> Tried emerging a bundle of packages and get conflicts relating to the
> USE=minimal, also resulted in some slot conflicts that I couldn't
> see. Its mostly the 'virtual/[pkg]' that require -minimal....
>
> emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage
> ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm lme4 glmnet rpart
> caret survival Hmisc rms epitools pwr TrialSize longpower simglm
> clusterPower samplesize PowerTOST blockrand bookdown ...
>
> !!! Multiple package instances within a single package slot have been pulled
> !!! into the dependency graph, resulting in a slot conflict:
>
> dev-lang/R:0
>
> The following USE changes are necessary to proceed:
> (see "package.use" in the portage(5) man page for more details)
> # required by sci-CRAN/survival-2.41.3::R_Overlay
> # required by sci-CRAN/multcomp-1.4.8::R_Overlay
> # required by sci-CRAN/rms-5.1.2::R_Overlay
> # required by rms (argument)
>>=dev-lang/R-3.4.4 minimal
>
> Strangely virtual/rpart is listed as requiring USE=-minimal but the
> rpart package itself requires USE=minimal.

The short answer is, reinstall R with USE=minimal.

Long story: dev-lang/R[-minimal] installs a set of R-recommended packages,

  https://cran.r-project.org/src/contrib/3.3.3/Recommended/

The packages are bundled with R.  Then some package foo in R_Overlay,
depends on Matrix-1.4.  It is not a problem for R, because it does not
track files and Matrix-1.4 overwrites the bundled Matrix-1.2.8.  Portage
is strict on file collisions.  Therefore, we have introduced the
virtuals.  If you read the virtual ebuilds, e.g. matrix, it speaks for
itself

DESCRIPTION="Virtual of a R recommended package"
RDEPEND="
        || (
                dev-lang/R[-minimal]
                sci-CRAN/Matrix
        )"

> 3. Missing ebuild for one package
> ==========================
>
> I was going to try emergeing the blogdown package (https://cran.r-project.org/web/packages/blogdown/) but there is no ebuild for it in
> R_Overlay...
>
> # emerge -av blogdown
>
> emerge: there are no ebuilds to satisfy "blogdown".
>
> emerge: searching for similar names...
> emerge: Maybe you meant any of these: sci-CRAN/bookdown,
> sci-BIOC/ballgown, app-admin/logmon?

Reading CRAN blogdown

SystemRequirements: Hugo (<https://gohugo.io>) and Pandoc
(<http://pandoc.org>)

The parser will not know it is hugo (not yet packaged in Gentoo) and
app-text/pandoc.

> One minor caeveat is that I'm using a locally bumped version of R as
> the bugreport I've filed for bumping in portage
> (https://bugs.gentoo.org/632364) hasn't been addressed yet. I'm
> currently using =dev-lang/R-3.4.4

Thanks for the bug report.

> I'm unsure how the ebuilds in R_Overlay are generated, is it
> automatically based on available builds?

Yes, it has been a Google summer of code project by André Erdmann
mentored by calchan:

  https://blogs.gentoo.org/calchan/2015/04/05/why-we-do-not-have-nor-want-r-packages-in-the-tree/

Now I find myself the only one left to do the server maintenance with
our infra team.

> Thanks for yours and others work on this, having R packages managed by
> portage is a real boon, as it removes the need to update.packages(ask
> = FALSE) so regularly.

You're welcome.  I myself is an active user of it.

> If there is something I can do to help please let me know.

Keep on discussion.

If you have a connection with R development team, can we talk to them to
impose a machine-readable format on the "SystemRequirements:"?

Cheers,
Benda
Reply | Threaded
Open this post in threaded view
|

Re: Errors installing Rcpp using R_Overlay

Neil Shephard
Hi Benda,

Thanks for the comprehensive reply and explanations.  

Whilst I've no existing contact with the R development team I will make inquiries about moving "SystemRequirements" from free text to a more machine-readable format.

I'm also keen to help provide feedback on R_Overlay and help with its development where I can, to which end I have as advised re-emerged =dev-lang/R-3.4.4 with USE=minimal and tried installing packages I use.  Quite a few packages still fail unfortunately, I'm emerging the following....


# Tidyverse...
emerge -av tidyverse 
# ggplot2 extensions
emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm
# Recommended (not necessarily the recommend version though, will pull in latest from CRAN)
emerge -av KernSmooth MASS Matrix boot class sci-CRAN/cluster sci-CRAN/codetools foreign lattice mgcv nlme nnet rpart spatial survival
# Modelling
emerge -av lme4 glmnet Hmisc rms epitools 
# Sample Size
emerge -av pwr TrialSize longpower simglm clusterPower samplesize PowerTOST 
# Miscellaneous
emerge -av blockrand bookdown sci-CRAN/shiny rmarkdown

Of particular note is that the Recommended packages (https://cran.r-project.org/src/contrib/3.4.4/Recommended/) that were explicitly removed by using USE=minimal emerge =dev-lang/R-3.4.4 they mostly failed to build.

A total of 69 packages failed to build directly, slightly more failed because some of these 69 were dependencies.  Of those that explicitly failed it appears (to me) that they fall into three groups...

1) Outdated ebuilds

Quite a few src packages could not be retrieved...

# grep '404 Not Found' /var/tmp/portage/sci-CRAN/*/temp/build.log -B3 | grep contrib
/var/tmp/portage/sci-CRAN/ggHorizon-0.1/temp/build.log---2018-03-22 10:10:21--  http://cran.r-project.org/src/contrib/ggHorizon_0.1.tar.gz
/var/tmp/portage/sci-CRAN/ggimage-0.0.2/temp/build.log---2018-03-22 10:10:35--  http://cran.r-project.org/src/contrib/ggimage_0.0.2.tar.gz
/var/tmp/portage/sci-CRAN/igraph-1.1.2/temp/build.log---2018-03-22 10:09:30--  http://cran.r-project.org/src/contrib/igraph_1.1.2.tar.gz
/var/tmp/portage/sci-CRAN/lubridate-1.7.0/temp/build.log---2018-03-26 11:15:41--  http://cran.r-project.org/src/contrib/lubridate_1.7.0.tar.gz
/var/tmp/portage/sci-CRAN/Rcpp-0.12.15/temp/build.log---2018-03-22 09:11:46--  http://cran.r-project.org/src/contrib/Rcpp_0.12.15.tar.gz
/var/tmp/portage/sci-CRAN/rgl-0.95.1441/temp/build.log---2018-03-26 11:23:58--  http://cran.r-project.org/src/contrib/rgl_0.95.1441.tar.gz
/var/tmp/portage/sci-CRAN/xml2-0.1.2/temp/build.log---2018-03-26 11:15:01--  http://cran.r-project.org/src/contrib/xml2_0.1.2.tar.gz

I suspect that this is down to the SystemRequirements issue you've highlighted exists meaning outdated ebuilds exist in R_Overlay.


2) Checksums failed

Three packages failed to emerge due to Checksums of the fetched src not matching

# grep 'checksum' -i /var/tmp/portage/sci-CRAN/*/temp/build.log -B60 | grep contrib
/var/tmp/portage/sci-CRAN/Matrix-1.2.12/temp/build.log---2018-03-26 12:34:13--  http://cran.r-project.org/src/contrib/Matrix_1.2-12.tar.gz
/var/tmp/portage/sci-CRAN/mvtnorm-1.0.7/temp/build.log---2018-03-26 12:33:25--  http://cran.r-project.org/src/contrib/mvtnorm_1.0-7.tar.gz
/var/tmp/portage/sci-CRAN/nloptr-1.0.4/temp/build.log---2018-03-26 12:33:05--  http://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz


3) 'File Not Found'

The majority failed after the build and installation had occurred within R and control had returned to Portage with "File Not Found" errors similar to the following...

 * Package:    sci-CRAN/abind-1.4.5
 * Repository: R_Overlay
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
* installing *source* package ‘abind’ ...
** package ‘abind’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (abind)
Traceback (most recent call last):
  File "/usr/lib/portage/python3.5/doins.py", line 611, in <module>
    sys.exit(main(sys.argv[1:]))
  File "/usr/lib/portage/python3.5/doins.py", line 602, in main
    os.path.dirname(source)):
  File "/usr/lib/portage/python3.5/doins.py", line 450, in _doins
    return install_runner.install_file(source, os.path.dirname(dest))
  File "/usr/lib/portage/python3.5/doins.py", line 386, in install_file
    return self._ins_runner.run(source, dest_dir)
  File "/usr/lib/portage/python3.5/doins.py", line 195, in run
    sstat = os.stat(source)
FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abindy'
 * ERROR: sci-CRAN/abind-1.4.5::R_Overlay failed (install phase):
 *   doins failed
 * 
 * If you need support, post the output of `emerge --info '=sci-CRAN/abind-1.4.5::R_Overlay'`,
 * the complete build log and the output of `emerge -pqv '=sci-CRAN/abind-1.4.5::R_Overlay'`.
 * The complete build log is located at '/var/tmp/portage/sci-CRAN/abind-1.4.5/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-CRAN/abind-1.4.5/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abind-1.4.5'
 * S: '/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abind-1.4.5'


Having looked at a few of these it appears there is a common theme as the files that can not be found all refer to the "/var/tmp/portage/sci-CRAN/[pkg]/work/[pkg]y" directory, that is the letter 'y' has been appended to the package name...

# grep 'FileNotFound'  /var/tmp/portage/sci-CRAN/*/temp/build.log 
/var/tmp/portage/sci-CRAN/abind-1.4.5/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/abind-1.4.5/work/abindy'
/var/tmp/portage/sci-CRAN/acepack-1.4.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/acepack-1.4.1/work/acepacky'
/var/tmp/portage/sci-CRAN/backports-1.1.2/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/backports-1.1.2/work/backportsy'
/var/tmp/portage/sci-CRAN/bitops-1.0.6-r1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/bitops-1.0.6-r1/work/bitopsy'
/var/tmp/portage/sci-CRAN/blockrand-1.3-r1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/blockrand-1.3-r1/work/blockrandy'
/var/tmp/portage/sci-CRAN/boot-1.3.20/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/boot-1.3.20/work/booty'
/var/tmp/portage/sci-CRAN/class-7.3.14/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/class-7.3.14/work/classy'
/var/tmp/portage/sci-CRAN/cluster-2.0.6/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/cluster-2.0.6/work/clustery'
/var/tmp/portage/sci-CRAN/codetools-0.2.15/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/codetools-0.2.15/work/codetoolsy'
/var/tmp/portage/sci-CRAN/cubature-1.3.11/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/cubature-1.3.11/work/cubaturey'
/var/tmp/portage/sci-CRAN/epitools-0.5.10/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/epitools-0.5.10/work/epitoolsy'
/var/tmp/portage/sci-CRAN/evaluate-0.10.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/evaluate-0.10.1/work/evaluatey'
/var/tmp/portage/sci-CRAN/fftwtools-0.9.8/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/fftwtools-0.9.8/work/fftwtoolsy'
/var/tmp/portage/sci-CRAN/forcats-0.3.0/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/forcats-0.3.0/work/forcatsy'
/var/tmp/portage/sci-CRAN/foreign-0.8.69/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/foreign-0.8.69/work/foreigny'
/var/tmp/portage/sci-CRAN/Formula-1.2.2/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/Formula-1.2.2/work/Formulay'
/var/tmp/portage/sci-CRAN/ggalt-0.4.0/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggalt-0.4.0/work/ggalty'
/var/tmp/portage/sci-CRAN/ggbeeswarm-0.6.0/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggbeeswarm-0.6.0/work/ggbeeswarmy'
/var/tmp/portage/sci-CRAN/ggExtra-0.7/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggExtra-0.7/work/ggExtray'
/var/tmp/portage/sci-CRAN/ggforce-0.1.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggforce-0.1.1/work/ggforcey'
/var/tmp/portage/sci-CRAN/gglasso-1.4/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/gglasso-1.4/work/gglassoy'
/var/tmp/portage/sci-CRAN/ggmosaic-0.1.2/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggmosaic-0.1.2/work/ggmosaicy'
/var/tmp/portage/sci-CRAN/ggnetwork-0.5.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggnetwork-0.5.1/work/ggnetworky'
/var/tmp/portage/sci-CRAN/ggrepel-0.7.0/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggrepel-0.7.0/work/ggrepely'
/var/tmp/portage/sci-CRAN/ggridges-0.4.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggridges-0.4.1/work/ggridgesy'
/var/tmp/portage/sci-CRAN/ggROC-1.0/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/ggROC-1.0/work/ggROCy'
/var/tmp/portage/sci-CRAN/highr-0.6/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/highr-0.6/work/highry'
/var/tmp/portage/sci-CRAN/hms-0.4.2/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/hms-0.4.2/work/hmsy'
/var/tmp/portage/sci-CRAN/iterators-1.0.9/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/iterators-1.0.9/work/iteratorsy'
/var/tmp/portage/sci-CRAN/jpeg-0.1.8-r1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/jpeg-0.1.8-r1/work/jpegy'
/var/tmp/portage/sci-CRAN/KernSmooth-2.23.15/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/KernSmooth-2.23.15/work/KernSmoothy'
/var/tmp/portage/sci-CRAN/lattice-0.20.35/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/lattice-0.20.35/work/latticey'
/var/tmp/portage/sci-CRAN/latticeExtra-0.6.28/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/latticeExtra-0.6.28/work/latticeExtray'
/var/tmp/portage/sci-CRAN/locfit-1.5.9.1-r1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/locfit-1.5.9.1-r1/work/locfity'
/var/tmp/portage/sci-CRAN/markdown-0.8/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/markdown-0.8/work/markdowny'
/var/tmp/portage/sci-CRAN/MASS-7.3.49/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/MASS-7.3.49/work/MASSy'
/var/tmp/portage/sci-CRAN/MatrixModels-0.4.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/MatrixModels-0.4.1/work/MatrixModelsy'
/var/tmp/portage/sci-CRAN/minqa-1.2.4/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/minqa-1.2.4/work/minqay'
/var/tmp/portage/sci-CRAN/mnormt-1.5.5/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/mnormt-1.5.5/work/mnormty'
/var/tmp/portage/sci-CRAN/nipals-0.4/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/nipals-0.4/work/nipalsy'
/var/tmp/portage/sci-CRAN/nlme-3.1.131.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/nlme-3.1.131.1/work/nlmey'
/var/tmp/portage/sci-CRAN/nnet-7.3.12/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/nnet-7.3.12/work/nnety'
/var/tmp/portage/sci-CRAN/png-0.1.7-r1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/png-0.1.7-r1/work/pngy'
/var/tmp/portage/sci-CRAN/polspline-1.1.12/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/polspline-1.1.12/work/polspliney'
/var/tmp/portage/sci-CRAN/proto-1.0.0/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/proto-1.0.0/work/protoy'
/var/tmp/portage/sci-CRAN/pwr-1.2.2/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/pwr-1.2.2/work/pwry'
/var/tmp/portage/sci-CRAN/rematch-1.0.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/rematch-1.0.1/work/rematchy'
/var/tmp/portage/sci-CRAN/rpart-4.1.13/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/rpart-4.1.13/work/rparty'
/var/tmp/portage/sci-CRAN/rstudioapi-0.7/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/rstudioapi-0.7/work/rstudioapiy'
/var/tmp/portage/sci-CRAN/samplesize-0.2.4/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/samplesize-0.2.4/work/samplesizey'
/var/tmp/portage/sci-CRAN/selectr-0.3.2/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/selectr-0.3.2/work/selectry'
/var/tmp/portage/sci-CRAN/shiny-1.0.5/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/shiny-1.0.5/work/shinyy'
/var/tmp/portage/sci-CRAN/SparseM-1.77/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/SparseM-1.77/work/SparseMy'
/var/tmp/portage/sci-CRAN/spatial-7.3.11/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/spatial-7.3.11/work/spatialy'
/var/tmp/portage/sci-CRAN/TeachingDemos-2.10/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/TeachingDemos-2.10/work/TeachingDemosy'
/var/tmp/portage/sci-CRAN/tiff-0.1.5-r1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/tiff-0.1.5-r1/work/tiffy'
/var/tmp/portage/sci-CRAN/TrialSize-1.3-r1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/TrialSize-1.3-r1/work/TrialSizey'
/var/tmp/portage/sci-CRAN/viridis-0.5.0/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/viridis-0.5.0/work/viridisy'
/var/tmp/portage/sci-CRAN/zoo-1.8.1/temp/build.log:FileNotFoundError: [Errno 2] No such file or directory: b'/var/tmp/portage/sci-CRAN/zoo-1.8.1/work/zooy'


As this is a looong post I've put my emerge --info into a Pastebin post https://pastebin.com/Zc44aF1K

Cheers,

Neil

--
Natural selection is a mechanism for generating an exceedingly high degree of improbability. - R.A. Fisher

Ignorance more frequently begets confidence than does knowledge - by Charles Darwin

PGP Public : https://pgp.mit.edu/pks/lookup?op=get&search=0x0E7ECE9C10D7B4A0

Website - http://kimura.no-ip.info/
Photos - http://www.flickr.com/photos/slackline/


On 22 March 2018 at 23:57, Benda Xu <[hidden email]> wrote:
Hi Neil,

Thank you!

Neil Shephard <[hidden email]> writes:

> Thanks for taking the time to resolve this, that has worked nicely and
> Rcpp now emerges.
>
> I continued trying to replace all the packages I have installed
> directly through R with emerges from R_Overlay and opted to emerge the
> meta-package tidyverse which pulls in a ton of packages as well as
> more explicit packages that aren't pulled in. In doing so I've
> encountered three problems....
>
> 1. Some ebuilds try to pull in old versions.

> 2. Some ebuilds from R_Overlay require "USE=minimal dev-lang/R" whilst
> others require "USE=-minimal dev-lang/R" which makes it difficult to
> emerge things.

> 3. I found one package that is on CRAN but for which there is no ebuild.
>
> 1. Old Versions
> ============
>
> I found the following old version were pulled in....
>
> | Package | R_Overlay Version | CRAN version |
> |-----------|-------------------|---------------|
> | xml2 | 0.1.2 | 1.2.0 |
> | lubridate | 1.7.0 | 1.7.3 |

This is because the parser fails on the new version.  Taking xml2 for
example, the "system requirements" field on CRAN is:

  libxml2: libxml2-dev (deb), libxml2-devel (rpm)

The parser did not know "(deb)" this maps to dev-libs/libxml2, nor it
could match 'libxml2-devel'.


Before I had to fix these cornor cases manually.  I am thinking of
exposing the configuration file so that users can contribute to the new
parsing rules.

> 2. dev-lang/R [-]minimal conflicts
> ==========================
>
> Tried emerging a bundle of packages and get conflicts relating to the
> USE=minimal, also resulted in some slot conflicts that I couldn't
> see. Its mostly the 'virtual/[pkg]' that require -minimal....
>
> emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage
> ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm lme4 glmnet rpart
> caret survival Hmisc rms epitools pwr TrialSize longpower simglm
> clusterPower samplesize PowerTOST blockrand bookdown ...
>
> !!! Multiple package instances within a single package slot have been pulled
> !!! into the dependency graph, resulting in a slot conflict:
>
> dev-lang/R:0
>
> The following USE changes are necessary to proceed:
> (see "package.use" in the portage(5) man page for more details)
> # required by sci-CRAN/survival-2.41.3::R_Overlay
> # required by sci-CRAN/multcomp-1.4.8::R_Overlay
> # required by sci-CRAN/rms-5.1.2::R_Overlay
> # required by rms (argument)
>>=dev-lang/R-3.4.4 minimal
>
> Strangely virtual/rpart is listed as requiring USE=-minimal but the
> rpart package itself requires USE=minimal.

The short answer is, reinstall R with USE=minimal.

Long story: dev-lang/R[-minimal] installs a set of R-recommended packages,

  https://cran.r-project.org/src/contrib/3.3.3/Recommended/

The packages are bundled with R.  Then some package foo in R_Overlay,
depends on Matrix-1.4.  It is not a problem for R, because it does not
track files and Matrix-1.4 overwrites the bundled Matrix-1.2.8.  Portage
is strict on file collisions.  Therefore, we have introduced the
virtuals.  If you read the virtual ebuilds, e.g. matrix, it speaks for
itself

DESCRIPTION="Virtual of a R recommended package"
RDEPEND="
        || (
                dev-lang/R[-minimal]
                sci-CRAN/Matrix
        )"

> 3. Missing ebuild for one package
> ==========================
>
> I was going to try emergeing the blogdown package (https://cran.r-project.org/web/packages/blogdown/) but there is no ebuild for it in
> R_Overlay...
>
> # emerge -av blogdown
>
> emerge: there are no ebuilds to satisfy "blogdown".
>
> emerge: searching for similar names...
> emerge: Maybe you meant any of these: sci-CRAN/bookdown,
> sci-BIOC/ballgown, app-admin/logmon?

Reading CRAN blogdown

SystemRequirements: Hugo (<https://gohugo.io>) and Pandoc
(<http://pandoc.org>)

The parser will not know it is hugo (not yet packaged in Gentoo) and
app-text/pandoc.

> One minor caeveat is that I'm using a locally bumped version of R as
> the bugreport I've filed for bumping in portage
> (https://bugs.gentoo.org/632364) hasn't been addressed yet. I'm
> currently using =dev-lang/R-3.4.4

Thanks for the bug report.

> I'm unsure how the ebuilds in R_Overlay are generated, is it
> automatically based on available builds?

Yes, it has been a Google summer of code project by André Erdmann
mentored by calchan:

  https://blogs.gentoo.org/calchan/2015/04/05/why-we-do-not-have-nor-want-r-packages-in-the-tree/

Now I find myself the only one left to do the server maintenance with
our infra team.

> Thanks for yours and others work on this, having R packages managed by
> portage is a real boon, as it removes the need to update.packages(ask
> = FALSE) so regularly.

You're welcome.  I myself is an active user of it.

> If there is something I can do to help please let me know.

Keep on discussion.

If you have a connection with R development team, can we talk to them to
impose a machine-readable format on the "SystemRequirements:"?

Cheers,
Benda

Reply | Threaded
Open this post in threaded view
|

Re: Errors installing Rcpp using R_Overlay

Benda Xu
Hi Neil,

Sorry to getting back to you late.  I have not forgotten these issues.

Neil Shephard <[hidden email]> writes:

> Thanks for the comprehensive reply and explanations.
>
> Whilst I've no existing contact with the R development team I will
> make inquiries about moving "SystemRequirements" from free text to a
> more machine-readable format.
>
> I'm also keen to help provide feedback on R_Overlay and help with its
> development where I can, to which end I have as advised re-emerged
> =dev-lang/R-3.4.4 with USE=minimal and tried installing packages I
> use. Quite a few packages still fail unfortunately, I'm emerging the
> following....
>
> [...]

> 1) Outdated ebuilds
>
> Quite a few src packages could not be retrieved...
>
> # grep '404 Not Found' /var/tmp/portage/sci-CRAN/*/temp/build.log -B3 | grep contrib
> /var/tmp/portage/sci-CRAN/ggHorizon-0.1/temp/build.log---2018-03-22 10:10:21-- http://cran.r-project.org/src/contrib/ggHorizon_0.1.tar.gz
> /var/tmp/portage/sci-CRAN/ggimage-0.0.2/temp/build.log---2018-03-22 10:10:35-- http://cran.r-project.org/src/contrib/ggimage_0.0.2.tar.gz
> /var/tmp/portage/sci-CRAN/igraph-1.1.2/temp/build.log---2018-03-22 10:09:30-- http://cran.r-project.org/src/contrib/igraph_1.1.2.tar.gz
> /var/tmp/portage/sci-CRAN/lubridate-1.7.0/temp/build.log---2018-03-26 11:15:41-- http://cran.r-project.org/src/contrib/lubridate_1.7.0.tar.gz
> /var/tmp/portage/sci-CRAN/Rcpp-0.12.15/temp/build.log---2018-03-22 09:11:46-- http://cran.r-project.org/src/contrib/Rcpp_0.12.15.tar.gz
> /var/tmp/portage/sci-CRAN/rgl-0.95.1441/temp/build.log---2018-03-26 11:23:58-- http://cran.r-project.org/src/contrib/rgl_0.95.1441.tar.gz
> /var/tmp/portage/sci-CRAN/xml2-0.1.2/temp/build.log---2018-03-26 11:15:01-- http://cran.r-project.org/src/contrib/xml2_0.1.2.tar.gz
>
> I suspect that this is down to the SystemRequirements issue you've
> highlighted exists meaning outdated ebuilds exist in R_Overlay.

I am exposing a set of unmatched strings in the description field at

   http://roverlay.dev.gentoo.org/unresolved.html

For example, I can see the rgl case,

> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'XQuartz (on OSX)'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'zlib(optional)'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'libpng (>=1.2.9'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'pandoc (>=1.14'
> 2018-05-27 05:06:10 INFO     DependencyResolver.UNRESOLVABLE: 0x7, 'needed for vignettes)'
> 2018-05-27 05:06:10 INFO     EbuildCreation.rgl.depres: Cannot satisfy dependencies!
> 2018-05-27 05:06:10 INFO     EbuildCreation.rgl: Cannot create an ebuild for this package (status=-2).
> 2018-05-27 05:06:10 DEBUG    OverlayCreator.R_Overlay.sci-CRAN.rgl: removing 0.99.16 from rgl

These are non-machine readable strings that calls for special
treatments.  We should make a better parser for these.

> 2) Checksums failed
>
> Three packages failed to emerge due to Checksums of the fetched src not matching
>
> # grep 'checksum' -i /var/tmp/portage/sci-CRAN/*/temp/build.log -B60 | grep contrib
> /var/tmp/portage/sci-CRAN/Matrix-1.2.12/temp/build.log---2018-03-26 12:34:13-- http://cran.r-project.org/src/contrib/Matrix_1.2-12.tar.gz
> /var/tmp/portage/sci-CRAN/mvtnorm-1.0.7/temp/build.log---2018-03-26 12:33:25-- http://cran.r-project.org/src/contrib/mvtnorm_1.0-7.tar.gz
> /var/tmp/portage/sci-CRAN/nloptr-1.0.4/temp/build.log---2018-03-26
> 12:33:05-- http://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz

Hmmm, it looks like the upstream has silently replaced the tarballs.  Duh.

> 3) 'File Not Found'
>
> The majority failed after the build and installation had occurred
> within R and control had returned to Portage with "File Not Found"
> errors similar to the following...

This has been my silly typo...  Now fixed.

Cheers,
Benda