I am trying to install RcppEigen on my uni's cluster and I get the following error. I

Huh? <div class="highlight highlight-source-shell notranslate position-relative ov

installation error: object 'pkgInfo' not found,about rcppcore/rcppeigen

Comments (15)

eddelbuettel commented on June 5, 2024

Huh?

edd@rob:~/git/rcppeigen(master)$ ag pkgInfo       # ag is a recursive grep on steroids
edd@rob:~/git/rcppeigen(master)$

No such symbol is part of the package so you have a different problem you appear to be misdiagnosing. Is there local staff for the cluster you could rely on?

I am closing this as it manifestedly is not an issue in our package.

from rcppeigen.

sefabey commented on June 5, 2024

Could be a misdiagnosis on my part. I'll consult local staff. Thanks.

from rcppeigen.

eddelbuettel commented on June 5, 2024

The problem is likely the dependency chain. So to diagnose, let's do it one by one. You started with broom so I reckon we have lme4 here and hence RcppEigen. Check them individually.

Sometimes it is as simple as 'reinstall the package' as the C++ compiler/library changes may induce subtle issues. Also: what type of cluster? Any binary packages from Debian or Ubuntu by chance or all from source?

(I see the EL now so RedHat based? I know less there...)

from rcppeigen.

sefabey commented on June 5, 2024

Thanks for offering help to diagnose the problem as I have been pulling my hair the past week. IT support is not available during Xmas break! Such inconvenient time to be having this error!

To provide some background, I must confess this error only started appearing after I did something I should not have done. I've been working on Supercomputing Wales cluster which works on Slurm (I provided some info about the system below but more than happy to provide more if you require).

[c.c1541911@cl1 ~]$ cat /etc/os-release
NAME="Red Hat Enterprise Linux Server"
VERSION="7.4 (Maipo)"
ID="rhel"
ID_LIKE="fedora"
VARIANT="Server"
VARIANT_ID="server"
VERSION_ID="7.4"
PRETTY_NAME="Red Hat Enterprise Linux Server 7.4 (Maipo)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:redhat:enterprise_linux:7.4:GA:server"
HOME_URL="https://www.redhat.com/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"

REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.4
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.4"

There is a nfshome drive where my .libpaths is located and there is a scratch drive(lustre methinks) where my data and scripts are stored.


> .libPaths()
[1] "/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5"
[2] "/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/library"

[c.c1541911@cl1 ~]$ cd /scratch/c.c1541911/muslim_islam_tweets/
[c.c1541911@cl1 muslim_islam_tweets]$ du -hsc *
15T	data
121M	parse_job
32K	src
15T	total
[c.c1541911@cl1 muslim_islam_tweets]$

Two days ago, I was processing some batch data on the scratch drive and exporting intermediate results to .rds files. I recognised an issue with intermediate .rds files and wanted to remove all .rds files on my scratch drive and re-process data. Stupidity begins here. Thinking I was in my data folder on the scratch drive, I executed find . -type f -name '*temp.rds' -delete. However, apparently, I was on my nfshome drive and I, inadvertently (read stupidly), removed all .rds files in my nfshome, hence in my .libPaths(). Naturally, my packages started not working. My scripts failed, the error being Error in library(tidy verse) : there is no package called ‘tidyverse’. I tried installing the tidyverse and it failed with object 'pkgInfo' not found error. Then I managed to re-install most tidyverse packages with the exception of broom. I tired re-installing broom, lme4 and I get the same "object 'pkgInfo' not found error". I tried tracking the issue by reading error messages and thought it was a RcppEigen issue but it might not be! That said Rcpp package seems to load fine. Any suggestions are appreciated!

> install.packages("lme4")
Installing package into ‘/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependency ‘RcppEigen’

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/RcppEigen_0.3.3.5.0.tar.gz'
Content type 'application/x-gzip' length 1633859 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/lme4_1.1-19.tar.gz'
Content type 'application/x-gzip' length 4120276 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** libs
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c RcppEigen.cpp -o RcppEigen.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c RcppExports.cpp -o RcppExports.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c fastLm.cpp -o fastLm.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -xHost  -c init.c -o init.o
icpc -shared -L/usr/local/lib64 -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o init.o -L/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/lib -lRlapack -L/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/lib -lRblas -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
installing to /nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  object 'pkgInfo' not found
ERROR: lazy loading failed for package ‘RcppEigen’
* removing ‘/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen’
ERROR: dependency ‘RcppEigen’ is not available for package ‘lme4’
* removing ‘/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/lme4’

The downloaded source packages are in
	‘/tmp/RtmppNWEih/downloaded_packages’
Warning messages:
1: In install.packages("lme4") :
  installation of package ‘RcppEigen’ had non-zero exit status
2: In install.packages("lme4") :
  installation of package ‘lme4’ had non-zero exit status

from rcppeigen.

eddelbuettel commented on June 5, 2024

That' still nested: lme4 calling RcppEigen. Figure out RcppEigen on its own. If it doesn't work look at its dependencies, maybe you need to repair Rcpp first?

(Gentle handwave. My wife has relatives in Wales and I visited the Rhonda valley years back. Am also a former slurm user and used to look after slurm too for Debian for a bit. Nice tool. But yes, large installations are fragile and you may be hosed now til admins come back / help with backups etc pp. At least you know it once worked so there is hope of getting it back eventually...)

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sefabey commented on June 5, 2024

Umm, how would one go about unnesting the issue? I tried unnesting the error by installing the RcppEigen and all it's dependencies but I still get the pkgInfo error.

> install.packages("RcppEigen", dependencies = c("Depends", "Imports","LinkingTo", "Suggests", "Enhances"))
Installing package into ‘/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/RcppEigen_0.3.3.5.0.tar.gz'
Content type 'application/x-gzip' length 1633859 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** libs
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c RcppEigen.cpp -o RcppEigen.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c RcppExports.cpp -o RcppExports.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c fastLm.cpp -o fastLm.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -xHost  -c init.c -o init.o
icpc -shared -L/usr/local/lib64 -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o init.o -L/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/lib -lRlapack -L/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/lib -lRblas -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
installing to /nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  object 'pkgInfo' not found
ERROR: lazy loading failed for package ‘RcppEigen’
* removing ‘/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen’

The downloaded source packages are in
	‘/tmp/RtmppNWEih/downloaded_packages’
Warning message:
In install.packages("RcppEigen", dependencies = c("Depends", "Imports",  :
  installation of package ‘RcppEigen’ had non-zero exit status

Despite this error, I checked my .libPaths() and there is not RcppEigen folder there! And as per your first message, the issue does not seem to be about RcppEigen but I can only track it back to RccpEigen! Must say, I am confused. To make the matters worse, not much search results return when I look for 'object 'pkgInfo' not found' online.

Re reparing Rcpp, the Rcpp pacakge loads without errors so I am not sure what should I explore further about that.

ATM, most of my scripts are working if I replace library(tidverse) with multitude of packages which is slightly annoying. I'm more worried about possible future consequences and obivouslt not being able to laod broom.

(Gentle Waveback: Rhondda is very nice! If you visit South Wales again and happen to have time for a chat, I can buy you a coffee and some Welsh cakes.)

from rcppeigen.

eddelbuettel commented on June 5, 2024

The loadNamespace failure is puzzling. It shouldn't try to look at other paths.

Just for our sanity: define a new first for entry for .libPaths, say ~/tmpRlib. Try installing Rcpp there. Then try installing RcppEigen.

(Sorry about the rookie spelling error with Rhondda. I should have known better. ;-)

from rcppeigen.

sefabey commented on June 5, 2024

Haha, Welsh spellings are always tricky!

I tried your suggestions, Rcpp installed and loaded fine again but RcppEigen keeps throwing the same error. Very curious indeed! I wonder what I managed to break so bad by removing .rds files that might result in this error.

Finally, I double checked and I don't have write access for the second .libPaths() (i.e. "/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/library") so the issue should be lie with my local library (methinks).

Change .libPaths()

> .libPaths()
[1] "/nfshome/store03/users/c.c1541911/R/x86_64-pc-linux-gnu-library/3.5"
[2] "/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/library"
> .libPaths("tmpRlib/")
> .libPaths()
[1] "/nfshome/store03/users/c.c1541911/tmpRlib"
[2] "/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/library"

Install and load Rcpp

> install.packages("Rcpp", dep
dependencies=  deparse
> install.packages("Rcpp", dependencies=TRUE)
Installing package into ‘/nfshome/store03/users/c.c1541911/tmpRlib’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

 1: 0-Cloud [https]                   2: Algeria [https]
 3: Australia (Canberra) [https]      4: Australia (Melbourne 1) [https]
 5: Australia (Melbourne 2) [https]   6: Australia (Perth) [https]
 7: Austria [https]                   8: Belgium (Ghent) [https]
 9: Brazil (PR) [https]              10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]            12: Brazil (SP 2) [https]
13: Bulgaria [https]                 14: Chile 1 [https]
15: Chile 2 [https]                  16: China (Hong Kong) [https]
17: China (Guangzhou) [https]        18: China (Lanzhou) [https]
19: China (Shanghai 1) [https]       20: China (Shanghai 2) [https]
21: Colombia (Cali) [https]          22: Czech Republic [https]
23: Denmark [https]                  24: East Asia [https]
25: Ecuador (Cuenca) [https]         26: Ecuador (Quito) [https]
27: Estonia [https]                  28: France (Lyon 1) [https]
29: France (Lyon 2) [https]          30: France (Marseille) [https]
31: France (Montpellier) [https]     32: France (Paris 2) [https]
33: Germany (Erlangen) [https]       34: Germany (Göttingen) [https]
35: Germany (Münster) [https]        36: Greece [https]
37: Iceland [https]                  38: India [https]
39: Indonesia (Jakarta) [https]      40: Ireland [https]
41: Italy (Padua) [https]            42: Japan (Tokyo) [https]
43: Japan (Yonezawa) [https]         44: Korea (Busan) [https]
45: Korea (Gyeongsan-si) [https]     46: Korea (Seoul 1) [https]
47: Korea (Ulsan) [https]            48: Malaysia [https]
49: Mexico (Mexico City) [https]     50: Norway [https]
51: Philippines [https]              52: Serbia [https]
53: Spain (A Coruña) [https]         54: Spain (Madrid) [https]
55: Sweden [https]                   56: Switzerland [https]
57: Turkey (Denizli) [https]         58: Turkey (Mersin) [https]
59: UK (Bristol) [https]             60: UK (London 1) [https]
61: USA (CA 1) [https]               62: USA (IA) [https]
63: USA (KS) [https]                 64: USA (MI 1) [https]
65: USA (NY) [https]                 66: USA (OR) [https]
67: USA (TN) [https]                 68: USA (TX 1) [https]
69: Uruguay [https]                  70: Vietnam [https]
71: (other mirrors)

Selection: 60
also installing the dependencies ‘evaluate’, ‘highr’, ‘markdown’, ‘yaml’, ‘xfun’, ‘htmltools’, ‘base64enc’, ‘jsonlite’, ‘mime’, ‘tinytex’, ‘RUnit’, ‘inline’, ‘rbenchmark’, ‘knitr’, ‘rmarkdown’, ‘pinp’, ‘pkgKitten’

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/evaluate_0.12.tar.gz'
Content type 'application/x-gzip' length 22639 bytes (22 KB)
==================================================
downloaded 22 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/highr_0.7.tar.gz'
Content type 'application/x-gzip' length 17505 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/markdown_0.9.tar.gz'
Content type 'application/x-gzip' length 80926 bytes (79 KB)
==================================================
downloaded 79 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/yaml_2.2.0.tar.gz'
Content type 'application/x-gzip' length 89447 bytes (87 KB)
==================================================
downloaded 87 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/xfun_0.4.tar.gz'
Content type 'application/x-gzip' length 48578 bytes (47 KB)
==================================================
downloaded 47 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/htmltools_0.3.6.tar.gz'
Content type 'application/x-gzip' length 45408 bytes (44 KB)
==================================================
downloaded 44 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/base64enc_0.1-3.tar.gz'
Content type 'application/x-gzip' length 7833 bytes
==================================================
downloaded 7833 bytes

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/jsonlite_1.6.tar.gz'
Content type 'application/x-gzip' length 1052728 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/mime_0.6.tar.gz'
Content type 'application/x-gzip' length 12960 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/tinytex_0.9.tar.gz'
Content type 'application/x-gzip' length 21012 bytes (20 KB)
==================================================
downloaded 20 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/RUnit_0.4.32.tar.gz'
Content type 'application/x-gzip' length 337142 bytes (329 KB)
==================================================
downloaded 329 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/inline_0.3.15.tar.gz'
Content type 'application/x-gzip' length 21455 bytes (20 KB)
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downloaded 20 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/rbenchmark_1.0.0.tar.gz'
Content type 'application/x-gzip' length 5093 bytes
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downloaded 5093 bytes

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/knitr_1.21.tar.gz'
Content type 'application/x-gzip' length 699667 bytes (683 KB)
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downloaded 683 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/rmarkdown_1.11.tar.gz'
Content type 'application/x-gzip' length 3148959 bytes (3.0 MB)
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downloaded 3.0 MB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/pinp_0.0.6.tar.gz'
Content type 'application/x-gzip' length 207158 bytes (202 KB)
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trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/pkgKitten_0.1.4.tar.gz'
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downloaded 7074 bytes

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/Rcpp_1.0.0.tar.gz'
Content type 'application/x-gzip' length 3635277 bytes (3.5 MB)
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downloaded 3.5 MB

* installing *source* package ‘evaluate’ ...
** package ‘evaluate’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (evaluate)
* installing *source* package ‘highr’ ...
** package ‘highr’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (highr)
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c api.c -o api.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c dumper.c -o dumper.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c emitter.c -o emitter.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c implicit.c -o implicit.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c loader.c -o loader.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c parser.c -o parser.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c r_emit.c -o r_emit.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c r_ext.c -o r_ext.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c r_parse.c -o r_parse.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c reader.c -o reader.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c scanner.c -o scanner.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I. -DNDEBUG  -I/usr/local/include   -fpic  -xHost  -c writer.c -o writer.o
icc -std=gnu99 -shared -L/usr/local/lib64 -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o
installing to /nfshome/store03/users/c.c1541911/tmpRlib/yaml/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (yaml)
* installing *source* package ‘xfun’ ...
** package ‘xfun’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xfun)
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** libs
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c base64.c -o base64.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c uriencode.c -o uriencode.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c utf8.c -o utf8.o
icc -std=gnu99 -shared -L/usr/local/lib64 -o base64enc.so base64.o uriencode.o utf8.o
installing to /nfshome/store03/users/c.c1541911/tmpRlib/base64enc/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (base64enc)
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** libs
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c base64.c -o base64.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c collapse_array.c -o collapse_array.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c collapse_object.c -o collapse_object.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c collapse_pretty.c -o collapse_pretty.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c escape_chars.c -o escape_chars.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c integer64_to_na.c -o integer64_to_na.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c is_datelist.c -o is_datelist.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c is_recordlist.c -o is_recordlist.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c is_scalarlist.c -o is_scalarlist.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c modp_numtoa.c -o modp_numtoa.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c null_to_na.c -o null_to_na.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c num_to_char.c -o num_to_char.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c parse.c -o parse.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c prettify.c -o prettify.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c push_parser.c -o push_parser.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c r-base64.c -o r-base64.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c register.c -o register.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c row_collapse.c -o row_collapse.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c transpose_list.c -o transpose_list.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c validate.c -o validate.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl.c -o yajl/yajl.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl_buf.c -o yajl/yajl_buf.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl_encode.c -o yajl/yajl_encode.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl_gen.c -o yajl/yajl_gen.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl_lex.c -o yajl/yajl_lex.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl_parser.c -o yajl/yajl_parser.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include    -fpic  -xHost  -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
icc -std=gnu99 -shared -L/usr/local/lib64 -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl
installing to /nfshome/store03/users/c.c1541911/tmpRlib/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (jsonlite)
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** libs
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c init.c -o init.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c rawmatch.c -o rawmatch.o
icc -std=gnu99 -shared -L/usr/local/lib64 -o mime.so init.o rawmatch.o
installing to /nfshome/store03/users/c.c1541911/tmpRlib/mime/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mime)
* installing *source* package ‘RUnit’ ...
** package ‘RUnit’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RUnit)
* installing *source* package ‘inline’ ...
** package ‘inline’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (inline)
* installing *source* package ‘rbenchmark’ ...
** package ‘rbenchmark’ successfully unpacked and MD5 sums checked
** R
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rbenchmark)
* installing *source* package ‘pkgKitten’ ...
** package ‘pkgKitten’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pkgKitten)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -xHost  -c Date.cpp -o Date.o
Date.cpp(642): warning #437: reference to local variable of enclosing function is not allowed
  		      2 * sizeof *sp + 4 * TZ_MAX_TIMES];
  		                  ^

icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -xHost  -c Module.cpp -o Module.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -xHost  -c Rcpp_init.cpp -o Rcpp_init.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -xHost  -c api.cpp -o api.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -xHost  -c attributes.cpp -o attributes.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -xHost  -c barrier.cpp -o barrier.o
icpc -shared -L/usr/local/lib64 -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o
installing to /nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
* installing *source* package ‘markdown’ ...
** package ‘markdown’ successfully unpacked and MD5 sums checked
** libs
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c Rbase64.c -o Rbase64.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c Rinit.c -o Rinit.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c Rmarkdown.c -o Rmarkdown.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c autolink.c -o autolink.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c buffer.c -o buffer.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c houdini_href_e.c -o houdini_href_e.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c houdini_html_e.c -o houdini_html_e.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c html.c -o html.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c html_smartypants.c -o html_smartypants.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c markdown.c -o markdown.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -xHost  -c stack.c -o stack.o
icc -std=gnu99 -shared -L/usr/local/lib64 -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdini_html_e.o html.o html_smartypants.o markdown.o stack.o
installing to /nfshome/store03/users/c.c1541911/tmpRlib/markdown/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (markdown)
* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** libs
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/include" -I/usr/local/include   -fpic  -xHost  -c RcppExports.cpp -o RcppExports.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/include" -I/usr/local/include   -fpic  -xHost  -c init.c -o init.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/include" -I/usr/local/include   -fpic  -xHost  -c template.cpp -o template.o
icpc -shared -L/usr/local/lib64 -o htmltools.so RcppExports.o init.o template.o
installing to /nfshome/store03/users/c.c1541911/tmpRlib/htmltools/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (htmltools)
* installing *source* package ‘tinytex’ ...
** package ‘tinytex’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (tinytex)
* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (knitr)
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rmarkdown)
* installing *source* package ‘pinp’ ...
** package ‘pinp’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pinp)

The downloaded source packages are in
	‘/tmp/RtmpNQIgEk/downloaded_packages’
> library(Rcpp)

Install fails for RcppEigen

> install.packages("RcppEigen", dependencies=TRUE)
Installing package into ‘/nfshome/store03/users/c.c1541911/tmpRlib’
(as ‘lib’ is unspecified)
also installing the dependency ‘microbenchmark’

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/microbenchmark_1.4-6.tar.gz'
Content type 'application/x-gzip' length 57682 bytes (56 KB)
==================================================
downloaded 56 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/RcppEigen_0.3.3.5.0.tar.gz'
Content type 'application/x-gzip' length 1633859 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘microbenchmark’ ...
** package ‘microbenchmark’ successfully unpacked and MD5 sums checked
checking for gcc... icc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether icc -std=gnu99 accepts -g... yes
checking for icc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... icc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for uint64_t... yes
checking for error_at_line... yes
checking for mach_absolute_time... no
checking for library containing clock_gettime... none required
checking for best clockid_t to use with clock_gettime... CLOCK_MONOTONIC_RAW
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -D_POSIX_C_SOURCE=200112L -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -xHost  -c do_nothing.c -o do_nothing.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -D_POSIX_C_SOURCE=200112L -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -xHost  -c init.c -o init.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG -D_POSIX_C_SOURCE=200112L -DHAVE_CONFIG_H  -I/usr/local/include   -fpic  -xHost  -c nanotimer.c -o nanotimer.o
icc -std=gnu99 -shared -L/usr/local/lib64 -o microbenchmark.so do_nothing.o init.o nanotimer.o
installing to /nfshome/store03/users/c.c1541911/tmpRlib/microbenchmark/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (microbenchmark)
* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** libs
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c RcppEigen.cpp -o RcppEigen.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c RcppExports.cpp -o RcppExports.o
icpc  -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/include" -I/usr/local/include  -I../inst/include -fpic  -xHost  -c fastLm.cpp -o fastLm.o
icc -std=gnu99 -I"/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/include" -DNDEBUG  -I"/nfshome/store03/users/c.c1541911/tmpRlib/Rcpp/include" -I/usr/local/include   -fpic  -xHost  -c init.c -o init.o
icpc -shared -L/usr/local/lib64 -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o init.o -L/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/lib -lRlapack -L/apps/languages/R/3.5.1/el7/AVX512/intel-2018/lib64/R/lib -lRblas -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
installing to /nfshome/store03/users/c.c1541911/tmpRlib/RcppEigen/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  object 'pkgInfo' not found
ERROR: lazy loading failed for package ‘RcppEigen’
* removing ‘/nfshome/store03/users/c.c1541911/tmpRlib/RcppEigen’

The downloaded source packages are in
	‘/tmp/RtmpNQIgEk/downloaded_packages’
Warning message:
In install.packages("RcppEigen", dependencies = TRUE) :
  installation of package ‘RcppEigen’ had non-zero exit status
>

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eddelbuettel commented on June 5, 2024

I recommend hard-wiring a mirror in your system-wide (maybe you can't) or personal .Rprofile:

edd@rob:~$ grep -C2 cloud /etc/R/Rprofile.site
#})

## We set the cloud mirror, which is 'network-close' to everybody, as default
local({
    r <- getOption("repos")
    r["CRAN"] <- "https://cloud.r-project.org"
    options(repos = r)
})
edd@rob:~$

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eddelbuettel commented on June 5, 2024

As for the RcppEigen error: beats me. Truly sorry but I don't think I can offer any more help here. It not something I have seen in 20+ years with R.

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sefabey commented on June 5, 2024

We set the cloud mirror, which is 'network-close' to everybody, as default local({ r <- getOption("repos") r["CRAN"] <- "https://cloud.r-project.org" options(repos = r) })

I'm sorry, could not help but notice the edited bit as it popped up in my email notifications. Have I done sth wrong? If so, my apologies. Never meant to waste your time.

Thanks for the .Rprofile suggestion, I'll try to do it.

As for RcppEigen, as a last resort, I tried a fresh .libPaths(), installing Rcpp only (w/o dependencies) and then RcppEigen (again, w/o dependencies) and still getting the same error. I'll send an email to my sysadmin and hope they can fix the issue. Regardless of the outcome, appreciate the help and thank you for your time.

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eddelbuettel commented on June 5, 2024

It's a weird error and I wish I could help you.

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sefabey commented on June 5, 2024

Thanks anyway. I passed the issue on to my sysadmin.

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sefabey commented on June 5, 2024

Hello again,

Just for the closure, I've managed to sort this issue out. I've deleted my .libPaths() completely and got R to prompt me to create a new one and after that, I managed to install RcppEigen (hence reverse dependencies) w/o problems. Although this still does not make sense as I had tried effectively the same by changing the .libPaths() previously but I'm so glad to get my packages to work, I do not mind to debug further.

Also your suggestion to add a CRAN mirror to .Rprofile worked perfectly (was hesitant bc of permisions). Lastly, was influenced by your first comment and I've been using ag since. I'm amazed how useful and fast it works. Thank you!

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eddelbuettel commented on June 5, 2024

Thanks for reporting back, and sorry for the woes. C++ does sometimes require rebuilds, and that is what you ran into. The fact that our depedency graphs get bigger does not help. But by drilling down one often manages to get to the cause. Glad you have it working.

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installation error: object 'pkgInfo' not found about rcppeigen HOT 15 CLOSED

Comments (15)

We set the cloud mirror, which is 'network-close' to everybody, as default local({ r <- getOption("repos") r["CRAN"] <- "https://cloud.r-project.org" options(repos = r) })

Related Issues (20)

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