[R] Missing dependencies in pkg installs
Martin Maechler
maechler at stat.math.ethz.ch
Thu Jun 22 09:38:56 CEST 2017
>>>>> David Winsemius <dwinsemius at comcast.net>
>>>>> on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>> 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
yes, but see also below ..
> 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.
why? It does assume you spend some time understanding what it
is talking about.
OTOH, it is *THE* official document on the topic, written and
constantly updated by the R core team.
Anyway: " ERROR: 'configure' exists but is not executable "
is I think a crucial piece of information .. it's from stringi's
installation failure, and the top level directory of stringi (1.1-5)
in a Unix like (ls -l with user group names removed) looks like:
-rw-r--r--. 1451 Apr 7 15:08 DESCRIPTION
-rw-r--r--. 6207 Apr 7 11:21 INSTALL
-rw-r--r--. 3580 Mar 21 13:29 LICENSE
-rw-r--r--. 63692 Apr 7 15:08 MD5
-rw-r--r--. 6204 Oct 24 2016 NAMESPACE
-rw-r--r--. 22407 Apr 7 11:44 NEWS
drwxr-xr-x. 8192 Mar 28 10:26 R
-rwxr-xr-x. 66 Apr 2 2015 cleanup
-rw-rw-r--. 32193 Apr 8 05:46 config.log
-rwxrwxr-x. 40648 Apr 8 05:46 config.status
-rwxr-xr-x. 173757 Apr 7 11:43 configure
-rw-r--r--. 669 Jun 23 2015 configure.win
drwxr-xr-x. 512 Apr 7 11:50 inst
drwxr-xr-x. 8192 Mar 28 10:26 man
drwxr-xr-x. 16384 Apr 8 05:47 src
Note the "x"s in the 'configure' line's " -rwxr-xr-x. ":
This means the file is executable and a reasonable shell can
just "call the file" and it will be executed, but that's the
part which failed for you.
.. this *is* peculiar as it looks like some of the standard Unix
tools may be misbehaving for you .. I assume it could be some OS
security "feature" playing against you..
>>
>>
>>> 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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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> David Winsemius
> Alameda, CA, USA
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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