[R] Error installing packages

Wed Oct 19 18:45:43 CEST 2016

I run into this type of problem quite frequently on Windows.
I see no rhyme or reason for when it happens.
It seems random as to which package it can't move.

The problem is at least a year old, and bit one of my students yesterday.

The specific is that there is a problem with copying from a temporary location

package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation
‘C:\Users\userid\Documents\R\win-library\3.3\file2bb4515e370d\Rcpp’ to
‘C:\Users\userid\Documents\R\win-library\3.3\Rcpp’

It isn't always Rcpp, although I think that is one of the more
frequently observed packages to display the problem.

Then there is a secondary problem that catches the attention of the
student.  Some other package that depends
on the missing one won't load.

I have three fixes:

1.  This usually works.  just do another
install.packages("Rcpp")

2.  This usually works when the first one doesn't

Keeping R open, manually move (with two Window Explorer windows) Rcpp from
C:\Users\userid\Documents\R\win-library\3.3\file2bb4515e370d\Rcpp
to
C:\Users\userid\Documents\R\win-library\3.3\Rcpp

3.  This is rarely needed because the first two usually work.
Copy the entire directory
C:\Users\userid\Documents\R\win-library\3.3\Rcpp
from one Windows computer onto a memory stick, and then
copy it from the memory stick to the other Windows computer.
It must be from Windows to Windows.  Method 3 will not work from Mac to Windows.

On Wed, Oct 19, 2016 at 11:31 AM, David Winsemius
<dwinsemius at comcast.net> wrote:
>
>> On Oct 19, 2016, at 4:54 AM, Kevin E. Thorpe <kevin.thorpe at utoronto.ca> wrote:
>>
>> Hello.
>>
>> I am posting this on behalf of one of my students who is getting error messages when installing some packages. I have not seen this before nor have I been able to replicate it. I'm including the relevant (I think) information. I get the students to install rms with dependencies. As you can see, rms does get installed but when the attempt is made to attach it, ggplot2 cannot be loaded. Thus I tried explicitly installing ggplot2 and you can see then ensuing errors below. I have included the sessionInfo() at the end.
>>
>> I hope someone can point me at a solution.
>>
>>
>> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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>>
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>>
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>>
>> > install.packages("rms",dependencies=TRUE)
>> Installing package into ‘C:/Users/Leticia/Documents/R/win-library/3.3’
>> (as ‘lib’ is unspecified)
>> --- Please select a CRAN mirror for use in this session ---
>> trying URL 'http://cran.utstat.utoronto.ca/bin/windows/contrib/3.3/rms_4.5-0.zip'
>> Content type 'application/zip' length 1074995 bytes (1.0 MB)
>> downloaded 1.0 MB
>>
>> package ‘rms’ successfully unpacked and MD5 sums checked
>>
>> The downloaded binary packages are in
>>        C:\Users\Leticia\AppData\Local\Temp\Rtmpa0q2o2\downloaded_packages
>> > library(rms)
>> Loading required package: Hmisc
>> Loading required package: lattice
>> Loading required package: survival
>> Loading required package: Formula
>> Loading required package: ggplot2
>> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
>>  there is no package called ‘Rcpp’
>
> When I try to debug the installation errors, I always first try to fix the first error. In this case it is because Rcpp was not installed. The use of dependencies=TRUE does not cause a recursive installation of dependencies of dependencies. I would have simply used:
>
> install.packages('Rcpp", dependencies=TRUE)
>
>
>> Error: package ‘ggplot2’ could not be loaded
>> > install.packages("ggplot2",dependencies=TRUE)
>
> That was not the problem.
>
>> Installing package into ‘C:/Users/Leticia/Documents/R/win-library/3.3’
>> (as ‘lib’ is unspecified)
>> also installing the dependency ‘maptools’
>>
>> trying URL 'http://cran.utstat.utoronto.ca/bin/windows/contrib/3.3/maptools_0.8-39.zip'
>> Content type 'application/zip' length 1816384 bytes (1.7 MB)
>> downloaded 0 bytes
>>
>> trying URL 'http://cran.utstat.utoronto.ca/bin/windows/contrib/3.3/ggplot2_2.1.0.zip'
>> Content type 'application/zip' length 1996146 bytes (1.9 MB)
>> downloaded 4096 bytes
>>
>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>  cannot open the connection
>> In addition: Warning messages:
>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>  downloaded length 0 != reported length 1816384
>> 2: In download.file(url, destfile, method, mode = "wb", ...) :
>>  downloaded length 4096 != reported length 1996146
>> 3: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
>> 4: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>  cannot open compressed file 'maptools/DESCRIPTION', probable reason 'No such file or directory'
>
> The second error suggests a temporary difficulty in the download process. I'm guessing the user will not encounter it on a second attempt.
>
>
> Best;
> David.
>
>> > library(rms)
>> Loading required package: Hmisc
>> Loading required package: ggplot2
>> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
>>  there is no package called ‘Rcpp’
>> Error: package ‘ggplot2’ could not be loaded
>> > session.info()
>> Error: could not find function "session.info"
>> > sessionInfo()
>> R version 3.3.1 (2016-06-21)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 10586)
>>
>> locale:
>> [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252
>> [4] LC_NUMERIC=C                    LC_TIME=English_Canada.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] Formula_1.2-1   survival_2.39-4 lattice_0.20-33
>>
>> loaded via a namespace (and not attached):
>> [1] Matrix_1.2-6  tools_3.3.1   gtable_0.2.0  splines_3.3.1 grid_3.3.1
>> >
>>
>> --
>> Kevin E. Thorpe
>> Head of Biostatistics,  Applied Health Research Centre (AHRC)
>> Li Ka Shing Knowledge Institute of St. Michael's Hospital
>> Assistant Professor, Dalla Lana School of Public Health
>> University of Toronto
>> email: kevin.thorpe at utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>>
>> ______________________________________________
>> 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.
>
> 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.