non zero exit when installing package, only tidyverse

Question

I've set up hosted RStudio on Ubunto and have loaded several packages already with no issues, including caret and lubridate.

However, when I tried to install tidyverse I get:

> install.packages("tidyverse", dependencies = T)
Installing package into ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz'
Content type 'application/x-gzip' length 61647 bytes (60 KB)
==================================================
downloaded 60 KB

* installing *source* package ‘tidyverse’ ...
** package ‘tidyverse’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘as.col_spec.NULL’, ‘as.col_spec.character’, ‘as.col_spec.col_spec’, ‘as.col_spec.default’, ‘as.col_spec.list’, ‘format.col_spec’, ‘output_column.POSIXt’, ‘output_column.default’, ‘output_column.double’, ‘print.col_spec’, ‘print.collector’, ‘print.date_names’, ‘print.locale’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) : 
  shared object ‘readr.so’ not found
ERROR: lazy loading failed for package ‘tidyverse’
* removing ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/3.4/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmpv6cOap/downloaded_packages’

After installing r and rstudio on Ubuntu I also installed r-base-dev, libcurl4-openssl-dev, libssl-dev and libxml2-dev. I did this following console messages after initially trying to install tidyverse.

How can I overcome this error and install tidyverse?

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8    
 [5] LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C             
 [9] LC_ADDRESS=C           LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
[1] caret_6.0-80    ggplot2_3.0.0   lattice_0.20-35 lubridate_1.7.4 dplyr_0.7.6    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18       tidyr_0.8.1        class_7.3-14       assertthat_0.2.0   ipred_0.9-7       
 [6] foreach_1.4.4      R6_2.2.2           plyr_1.8.4         backports_1.1.2    magic_1.5-9       
[11] stats4_3.4.4       pillar_1.3.0       rlang_0.2.2        lazyeval_0.2.1     rstudioapi_0.7    
[16] data.table_1.11.6  kernlab_0.9-27     rpart_4.1-13       Matrix_1.2-12      splines_3.4.4     
[21] CVST_0.2-2         ddalpha_1.3.4      gower_0.1.2        stringr_1.3.1      munsell_0.5.0     
[26] broom_0.5.0        compiler_3.4.4     pkgconfig_2.0.2    dimRed_0.1.0       nnet_7.3-12       
[31] tidyselect_0.2.4   tibble_1.4.2       prodlim_2018.04.18 DRR_0.0.3          codetools_0.2-15  
[36] RcppRoll_0.3.0     crayon_1.3.4       withr_2.1.2        MASS_7.3-49        recipes_0.1.3     
[41] ModelMetrics_1.2.0 grid_3.4.4         nlme_3.1-131       gtable_0.2.0       magrittr_1.5      
[46] scales_1.0.0       stringi_1.2.4      reshape2_1.4.3     bindrcpp_0.2.2     timeDate_3043.102 
[51] robustbase_0.93-3  geometry_0.3-6     pls_2.7-0          lava_1.6.3         iterators_1.0.10  
[56] tools_3.4.4        glue_1.3.0         DEoptimR_1.0-8     purrr_0.2.5        sfsmisc_1.1-2     
[61] abind_1.4-5        survival_2.41-3    yaml_2.2.0         colorspace_1.3-2   bindr_0.1.1

score 1 · Accepted Answer · 2018-09-27T20:08:33.153

1

Looks like an issue with readr...

Error in library.dynam(lib, package, package.lib) : 
  shared object ‘readr.so’ not found

Use the code below to check if the package is installed. If not, it will be installed

#Specify packages
packages = c("readr")

package.check <- lapply(packages, FUN = function(x) {
  if (!require(x, character.only = TRUE)) {
    install.packages(x, dependencies = TRUE)
    library(x, character.only = TRUE)
  }
})

#Verify they are loaded
search()

If it is installed, the file may be locked...

#If "failed to create lock" is the returned error, install with the below code;
install.packages("readr", dependencies=TRUE, INSTALL_opts = c('--no-lock'))

(https://github.com/tidyverse/tidyverse/issues/99)

edited Sep 27 '18 at 20:08

answered Sep 27 '18 at 19:58

Good research, but you should probably cite [the GitHub issue](https://github.com/tidyverse/tidyverse/issues/99) you quote the last two lines of code from – duckmayr Sep 27 '18 at 20:05
@duckmayr, sorry, forgot to add! Thanks – Sep 27 '18 at 20:07
No problem, +1 now that the cite's there – duckmayr Sep 27 '18 at 20:08
'failed to create lock' with your first snippet so I ran your second snippet. The console has been running with the red dot since just after you provided your answer. Seems the console is not responding or something. I rebooted once already. It just lingers on ```* installing *source* package ‘readr’ ... ** package ‘readr’ successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/home/rstudio/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/home/rstudio/R/x86_64-pc-linux-gnu-library/... [lots of output here...]`` – Doug Fir Sep 27 '18 at 20:36
@DougFir To clarify, there is a last line of "[lots of output here...]" that it has not gone past in some time? – duckmayr Sep 27 '18 at 20:42
@duckmayr yes that's correct. Here, I'll try to paste the rest (it's actually not a lot" ```g++ -I/usr/share/R/include -DNDEBUG -I"/home/rstudio/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/home/rstudio/R/x86_64-pc-linux-gnu-library/3.4/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Collector.cpp -o Collector.o``` – Doug Fir Sep 27 '18 at 20:47
@DougFir How much RAM do you have? – duckmayr Sep 27 '18 at 20:49
@duckmayr I tried to find out in AWS EC2 interface but could not see it. In the terminal I typed ```top | grep -i mem``` which gave 1007540. Does this indicate RAM? – Doug Fir Sep 27 '18 at 20:57
1

@DougFir Yeah. It looks like you don't have enough RAM to compile `readr` (see [this Stack Overflow question](https://stackoverflow.com/a/40949665/8386140) and [this GitHub issue](https://github.com/tidyverse/readr/issues/544)). If you follow the instructions of the top answer to the Stack Overflow question I linked, I think you should be alright. – duckmayr Sep 27 '18 at 21:02

non zero exit when installing package, only tidyverse

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