[R] Missing dependencies in pkg installs

David Winsemius dwinsemius at comcast.net
Thu Jun 22 03:04:13 CEST 2017


> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK) <Mike.Conklin at gfk.com> wrote:
> 
> I have a Ubuntu server with an R installation that has 384 packages installed.  We are trying to replicate the system on a Red Hat Enterprise server. I downloaded the list of packages from the Ubuntu machine and read it into an R session on the new machine. Then I ran install.packages(listofpackages).  Now I have 352 packages on the new machine but several very common packages (like much of the tidyverse, ggplot2, Hmisc) failed to install because of missing dependencies (most of which are the other packages that failed to install).
> 
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-redhat-linux-gnu (64-bit)

I'd make sure you have reviewed this:

https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essential-programs-and-libraries

Best;
David.

> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
> 
> Matrix products: default
> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] dplyr_0.7.0 shiny_1.0.3
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0   magrittr_1.5     assertthat_0.2.0 R6_2.2.2
> [5] htmltools_0.3.6  tools_3.4.0      glue_1.1.1       tibble_1.3.3
> [9] Rcpp_0.12.11     digest_0.6.12    xtable_1.8-2     httpuv_1.3.3
> [13] mime_0.5         rlang_0.1.1
>> 
> 
> 
> If I try and install Hmisc for example I get the following errors:
> for the first error ERROR: 'configure' exists but is not executable -- see the 'R Installation and dministration Manual'  I did not find the R Installation and Administration Manual helpful.
> 
> 
>> install.packages("Hmisc")
> Installing package into '/usr/lib64/R/library'
> (as 'lib' is unspecified)
> also installing the dependencies 'stringi', 'evaluate', 'reshape2', 'stringr', knitr', 'ggplot2', 'htmlTable', 'viridis'
> 
> trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
> Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
> ==================================================
> downloaded 3.5 MB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
> Content type 'application/x-gzip' length 21914 bytes (21 KB)
> ==================================================
> downloaded 21 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
> Content type 'application/x-gzip' length 34688 bytes (33 KB)
> ==================================================
> downloaded 33 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.2.0.tar.gz'
> Content type 'application/x-gzip' length 94095 bytes (91 KB)
> ==================================================
> downloaded 91 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.16.tar.gz'
> Content type 'application/x-gzip' length 1031259 bytes (1007 KB)
> ==================================================
> downloaded 1007 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz'
> Content type 'application/x-gzip' length 2213308 bytes (2.1 MB)
> ==================================================
> downloaded 2.1 MB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/htmlTable_1.9.tar.gz'
> Content type 'application/x-gzip' length 152095 bytes (148 KB)
> ==================================================
> downloaded 148 KB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz'
> Content type 'application/x-gzip' length 1787731 bytes (1.7 MB)
> ==================================================
> downloaded 1.7 MB
> 
> trying URL 'https://cloud.r-project.org/src/contrib/Hmisc_4.0-3.tar.gz'
> Content type 'application/x-gzip' length 702759 bytes (686 KB)
> ==================================================
> downloaded 686 KB
> 
> * installing *source* package 'stringi' ...
> ** package 'stringi' successfully unpacked and MD5 sums checked
> ERROR: 'configure' exists but is not executable -- see the 'R Installation and dministration Manual'
> * removing '/usr/lib64/R/library/stringi'
> ERROR: dependency 'stringi' is not available for package 'stringr'
> * removing '/usr/lib64/R/library/stringr'
> ERROR: dependency 'stringr' is not available for package 'evaluate'
> * removing '/usr/lib64/R/library/evaluate'
> ERROR: dependency 'stringr' is not available for package 'reshape2'
> * removing '/usr/lib64/R/library/reshape2'
> ERROR: dependencies 'evaluate', 'stringr' are not available for package 'knitr'
> * removing '/usr/lib64/R/library/knitr'
> ERROR: dependency 'reshape2' is not available for package 'ggplot2'
> * removing '/usr/lib64/R/library/ggplot2'
> ERROR: dependencies 'stringr', 'knitr' are not available for package 'htmlTable
> * removing '/usr/lib64/R/library/htmlTable'
> ERROR: dependency 'ggplot2' is not available for package 'viridis'
> * removing '/usr/lib64/R/library/viridis'
> ERROR: dependencies 'ggplot2', 'htmlTable', 'viridis' are not available for pacage 'Hmisc'
> * removing '/usr/lib64/R/library/Hmisc'
> 
> 
> Any help is appreciated.
> --
> W. Michael Conklin
> Executive Vice President
> Marketing & Data Sciences - North America
> GfK | 8401 Golden Valley Road | Minneapolis | MN | 55427
> mike.conklin at gfk.com<mailto:mike.conklin at gfk.com>
> T +1 763 417 4545 | M +1 612 567 8287
> www.gfk.com<http://www.gfk.com/>
> 
> 
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> 
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David Winsemius
Alameda, CA, USA



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