I am using debug on the .install_packages function...stepping through. Once the
temporary folder is created and the tar file expanded I run file_test and get a
FALSE back indicating that the configure file is not executable.
[1] "/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi"
Browse[2]> dir(new)
[1] "DESCRIPTION" "INSTALL" "LICENSE" "MD5"
[5] "NAMESPACE" "NEWS" "R" "cleanup"
[9] "configure" "configure.win" "inst" "man"
[13] "src"
Browse[2]> test_file("-x",paste0(new,"/configure")
+ )
Error in test_file("-x", paste0(new, "/configure")) :
could not find function "test_file"
Browse[2]> file_test("-x",paste0(new,"/configure"))
/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi/configure
FALSE
However, at the same time, in a separate session I have the system look at the
very same file and clearly the execution bit is set.
[root@dcex1102shinypr ~]# ls -l /tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi
total 312
-rwxr-xr-x 1 root root 66 Apr 2 2015 cleanup
-rwxr-xr-x 1 root root 173757 Apr 7 11:43 configure
-rw-r--r-- 1 root root 669 Jun 23 2015 configure.win
-rw-r--r-- 1 root root 1451 Apr 7 15:08 DESCRIPTION
drwxr-xr-x 2 root root 35 Jun 22 22:26 inst
-rw-r--r-- 1 root root 6207 Apr 7 11:21 INSTALL
-rw-r--r-- 1 root root 3580 Mar 21 13:29 LICENSE
drwxr-xr-x 2 root root 4096 Jun 22 22:26 man
-rw-r--r-- 1 root root 63692 Apr 7 15:08 MD5
-rw-r--r-- 1 root root 6204 Oct 24 2016 NAMESPACE
-rw-r--r-- 1 root root 22407 Apr 7 11:44 NEWS
drwxr-xr-x 2 root root 4096 Jun 22 22:26 R
drwxr-xr-x 3 root root 8192 Jun 22 22:26 src
[root@dcex1102shinypr ~]#
If I CTRL-Z out of R in the first session I confirm the same result - the
system shows the file as executable
--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK
T +1 763 417 4545 | M +1 612 567 8287
-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Thursday, June 22, 2017 3:06 PM
To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] Missing dependencies in pkg installs
On 22/06/2017 3:42 PM, Conklin, Mike (GfK) wrote:
> Not much progress..... I step through debug and it gets to the do.install()
> function which immediately errors with the same "configuration not
> executable" error.
I believe that is a locally defined function, which means you can set a
breakpoint within it but only if R is compiled with source info, or you can
manually call debug(do_install) after it has been created (typically just
before it is called is a safe place to do this), and do the usual process.
It's still very mysterious to me why configure is losing its executable bit.
What I would do if I could reproduce this would be to run right up to the
file_test("-x","configure") line, then print my working directory, and ctrl-Z
out of R to look at the files there. That should confirm that configure is not
executable.
Then the hard part is figuring out why it isn't....
Duncan
>
> So, made a tempfunc that was a copy of tools:::.install_packages and
> edited the file_test("-x","configure") line to return a TRUE
>
> now I get a Permission Denied error (even if I run as root)
>
>> tempfunc("/home/meconk/stringi_1.1.5.tar.gz")
> * installing to library '/usr/lib64/R/library'
> * installing *source* package 'stringi' ...
> ** package 'stringi' successfully unpacked and MD5 sums checked
> sh: ./configure: Permission denied
> ERROR: configuration failed for package 'stringi'
> * removing '/usr/lib64/R/library/stringi'
> Error in do_exit(status = status) : .install_packages() exit status 1
> Error in do_exit(status = status) : .install_packages() exit status 1
>
> --
> W. Michael Conklin
> EVP Marketing & Data Sciences
> GfK
> T +1 763 417 4545 | M +1 612 567 8287
>
>
> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Thursday, June 22, 2017 11:09 AM
> To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
> Cc: r-help@r-project.org
> Subject: Re: [R] Missing dependencies in pkg installs
>
> On 22/06/2017 11:15 AM, Conklin, Mike (GfK) wrote:
>> Following Duncan's instructions I find that the system and R find that
>> configure IS executable but if trying to install via install.packages I get
>> the same error.
>> I also tried using R CMD INSTALL from the terminal and install.packages with
>> a local file pointing to the very same tar.gz file that shows the executable
>> bit set. All result in the same "configure is not executable" result.
>>
>
> That's very mysterious. This is hard to debug, because R runs a separate
> process to do the installs. If you want to track this down you can debug the
> code as follows.
>
> 1. Manually download the tarball, using any method (perhaps
> download.packages("stringi", destdir = ".", type = "source").
>
> 2. In R, run
>
> debug(tools:::.install_packages)
> tools:::.install_packages("stringi_1.1.5.tar.gz")
>
> You can single step until you see the message, and try to diagnose why it is
> happening.
>
> Watch out, this function will exit R at the end.
>
> Duncan Murdoch
>
>> [meconk@dcex1102shinypr ~]$ ls -l stringi/configure -rwxr-xr-x 1
>> meconk meconk 173757 Apr 7 11:43 stringi/configure
>> [meconk@dcex1102shinypr ~]$ sudo R [sudo] password for meconk:
>>
>> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and 'citation()' on how to
>> cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> [Previously saved workspace restored]
>>
>>> getwd()
>> [1] "/home/meconk"
>>> file_test("-x","stringi/configure")
>> stringi/configure
>> TRUE
>>> install.packages("stringi")
>>> Installing package into '/usr/lib64/R/library'
>> (as 'lib' is unspecified)
>> 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
>>
>> * installing *source* package 'stringi' ...
>> ** package 'stringi' successfully unpacked and MD5 sums checked
>> ERROR: 'configure' exists but is not executable -- see the 'R Installation
>> and Administration Manual'
>> * removing '/usr/lib64/R/library/stringi'
>>
>> The downloaded source packages are in
>> '/tmp/Rtmpxw9twb/downloaded_packages'
>> Updating HTML index of packages in '.Library'
>> Making 'packages.html' ... done
>> Warning message:
>> In install.packages("stringi") :
>> installation of package 'stringi' had non-zero exit status
>>
>> --
>> W. Michael Conklin
>> EVP Marketing & Data Sciences
>> GfK
>> T +1 763 417 4545 | M +1 612 567 8287
>>
>> -----Original Message-----
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>> Duncan Murdoch
>> Sent: Thursday, June 22, 2017 8:23 AM
>> To: Martin Maechler; David Winsemius
>> Cc: r-help@r-project.org
>> Subject: Re: [R] Missing dependencies in pkg installs
>>
>> The "configure exists but is not executable" problem is somewhat
>> common on Windows, because there's usually no such thing as an
>> executable bit there. (Cygwin does something to fake one, but
>> Windows generally
>> doesn't.) If you create a tarball there by default you get no executable
>> bits marked in it.
>>
>> For a long time, R CMD build has dealt with this issue by using the internal
>> tar() function. It corrects the executable bit with a warning during the
>> build.
>>
>> So if people are getting that error, something has gone wrong. A few
>> guesses:
>>
>> - They are on Linux but using a mount of a Windows volume that doesn't
>> preserve the bit.
>>
>> - They are using a tarball produced in some strange way on Windows, e.g.
>> by calling tar directly instead of R CMD build.
>>
>> - There's a bug in R in detecting the executable bit.
>>
>> Martin saw configure marked executable in the tarball from CRAN,
>> which means the second is unlikely (unless it was very recently
>> fixed), but the first is still possible. One test is to manually
>> expand the tarball, then use both ls and R's test to see if the
>> executable bit is set and is detected by R. For example, after
>> downloading stringi_1.1.5.tar.gz you expand it using
>>
>> tar zxvf stringi_1.1.5.tar.gz
>>
>> and use
>>
>> ls -l stringi/configure
>>
>> to see if the system thinks it is executable, and in R,
>>
>> file_test("-x", "stringi/configure")
>>
>> to see what R sees.
>>
>> Duncan Murdoch
>>
>> On 22/06/2017 3:38 AM, Martin Maechler wrote:
>>>>>>>> David Winsemius <dwinsem...@comcast.net>
>>>>>>>> on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>>>
>>> >> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)
>>> <mike.conk...@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#Essent
>>> i
>>> a
>>> l-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.conk...@gfk.com<mailto:mike.conk...@gfk.com>
>>> >> T +1 763 417 4545 | M +1 612 567 8287
>>> >> www.gfk.com<http://www.gfk.com/>
>>> >>
>>> >>
>>> >> [[alternative HTML version deleted]]
>>> >>
>>> >> ______________________________________________
>>> >> R-help@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.
>>>
>>> > David Winsemius
>>> > Alameda, CA, USA
>>>
>>> > ______________________________________________
>>> > R-help@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.
>>>
>>> ______________________________________________
>>> R-help@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.
>>>
>>
>> ______________________________________________
>> R-help@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.
>>
>
______________________________________________
R-help@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.
