Re: [R-pkg-devel] Saving output of check()
I have at various times tried the built-in (tools package) solution;
fairly complex hand-rolled stuff I did myself; and revdepcheck. I found
that revdepcheck handled installation of needed dependencies, including
caching packages where necessary, more easily. It felt like the 'tools'
machinery worked better if I already had all or most of the CRAN
packages installed ... (My experimentation has been done
non-systematically and over a long period of time, so I may well have
mistaken/missed something.)
On 2018-04-11 06:03 PM, Uwe Ligges wrote:
> Not sure why nobody dicusses the R internal check functionality, also
> for reverse dependencies, from the tools package?
> That is what CRAN uses for the reverse dependency checks.
>
> Best,
> Uwe Ligges
>
>
>
>
> On 11.04.2018 23:14, J C Nash wrote:
>> Another workaround is to use
>>
>> tlogl <- readLines(attr(cpkg.chk, "path"))
>>
>> Possibly this may suggest a way to improve functionality.
>>
>> JN
>>
>> On 2018-04-11 03:24 PM, Henrik Bengtsson wrote:
>>> R CMD check, which is used internally runs checks in standalone
>>> background R processes. Output from these is not capturable/sinkable
>>> by the master R process. The gist of what's happening is:
>>>
sink("output.log")
system("echo hello") ## not sinked/captured
>>> hello
sink()
readLines("output.log")
>>> character(0)
>>>
>>> /Henrik
>>>
>>> On Wed, Apr 11, 2018 at 11:05 AM, J C Nash wrote:
Hi,
In trying to test that an upgrade to my optimx package does not
break other
packages, I wanted to loop over a list of all such packages in
alldep, with
nall the length of this list.
cat("Check the dependent packages\n")
for (ii in 1:nall){
cpkg <- alldep[ii]
dd <- "/home/john/temp/wrkopt/dlpkg"
dlname <- download.packages(cpkg, destdir=dd )[[2]]
cat("Downloaded ", dlname,"\n")
cpkg.chk <- devtools::check_built(dlname)
cat("Results package:",cpkg,"\n")
print(cpkg.chk)
}
Before running this, I did
sink("dpkgcheck.txt", split=TRUE)
and afterwards, I did sink().
But ... none of the check output, nor the result of the final print,
show
up in the output file dpkgcheck.txt.
Have I totally misunderstood sink(), or is there a nasty bug?
I've tried running in Rstudio and in the terminal. I'm running Linux
Mint
18.3 Sylvia.
Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10
16:32:20 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
john@john-j6-18 ~ $ R
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
J C Nash
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
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R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] Saving output of check()
Not sure why nobody dicusses the R internal check functionality, also
for reverse dependencies, from the tools package?
That is what CRAN uses for the reverse dependency checks.
Best,
Uwe Ligges
On 11.04.2018 23:14, J C Nash wrote:
Another workaround is to use
tlogl <- readLines(attr(cpkg.chk, "path"))
Possibly this may suggest a way to improve functionality.
JN
On 2018-04-11 03:24 PM, Henrik Bengtsson wrote:
R CMD check, which is used internally runs checks in standalone
background R processes. Output from these is not capturable/sinkable
by the master R process. The gist of what's happening is:
sink("output.log")
system("echo hello") ## not sinked/captured
hello
sink()
readLines("output.log")
character(0)
/Henrik
On Wed, Apr 11, 2018 at 11:05 AM, J C Nash wrote:
Hi,
In trying to test that an upgrade to my optimx package does not break other
packages, I wanted to loop over a list of all such packages in alldep, with
nall the length of this list.
cat("Check the dependent packages\n")
for (ii in 1:nall){
cpkg <- alldep[ii]
dd <- "/home/john/temp/wrkopt/dlpkg"
dlname <- download.packages(cpkg, destdir=dd )[[2]]
cat("Downloaded ", dlname,"\n")
cpkg.chk <- devtools::check_built(dlname)
cat("Results package:",cpkg,"\n")
print(cpkg.chk)
}
Before running this, I did
sink("dpkgcheck.txt", split=TRUE)
and afterwards, I did sink().
But ... none of the check output, nor the result of the final print, show
up in the output file dpkgcheck.txt.
Have I totally misunderstood sink(), or is there a nasty bug?
I've tried running in Rstudio and in the terminal. I'm running Linux Mint
18.3 Sylvia.
Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10 16:32:20
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
john@john-j6-18 ~ $ R
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
J C Nash
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Saving output of check()
Indeed these are useful for one of my present tasks. Thanks. JN
On 2018-04-11 03:10 PM, Georgi Boshnakov wrote:
>
> Hi,
>
> Not really an answer but I only recently discovered devtools::revdep(),
> which automates checking reverse dependencies.
>
> Georgi Boshnakov
>
>
>
>
>
> From: R-package-devel [r-package-devel-boun...@r-project.org] on behalf of J
> C Nash [profjcn...@gmail.com]
> Sent: 11 April 2018 19:05
> To: List r-package-devel
> Subject: [R-pkg-devel] Saving output of check()
>
> Hi,
>
> In trying to test that an upgrade to my optimx package does not break other
> packages, I wanted to loop over a list of all such packages in alldep, with
> nall the length of this list.
>
> cat("Check the dependent packages\n")
> for (ii in 1:nall){
> cpkg <- alldep[ii]
> dd <- "/home/john/temp/wrkopt/dlpkg"
> dlname <- download.packages(cpkg, destdir=dd )[[2]]
> cat("Downloaded ", dlname,"\n")
> cpkg.chk <- devtools::check_built(dlname)
> cat("Results package:",cpkg,"\n")
> print(cpkg.chk)
> }
>
> Before running this, I did
>
> sink("dpkgcheck.txt", split=TRUE)
>
> and afterwards, I did sink().
>
> But ... none of the check output, nor the result of the final print, show
> up in the output file dpkgcheck.txt.
>
> Have I totally misunderstood sink(), or is there a nasty bug?
>
> I've tried running in Rstudio and in the terminal. I'm running Linux Mint
> 18.3 Sylvia.
>
> Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10 16:32:20
> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
> john@john-j6-18 ~ $ R
>
> R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
>
>
> J C Nash
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Saving output of check()
Another workaround is to use
tlogl <- readLines(attr(cpkg.chk, "path"))
Possibly this may suggest a way to improve functionality.
JN
On 2018-04-11 03:24 PM, Henrik Bengtsson wrote:
> R CMD check, which is used internally runs checks in standalone
> background R processes. Output from these is not capturable/sinkable
> by the master R process. The gist of what's happening is:
>
>> sink("output.log")
>> system("echo hello") ## not sinked/captured
> hello
>> sink()
>> readLines("output.log")
> character(0)
>
> /Henrik
>
> On Wed, Apr 11, 2018 at 11:05 AM, J C Nash wrote:
>> Hi,
>>
>> In trying to test that an upgrade to my optimx package does not break other
>> packages, I wanted to loop over a list of all such packages in alldep, with
>> nall the length of this list.
>>
>> cat("Check the dependent packages\n")
>> for (ii in 1:nall){
>> cpkg <- alldep[ii]
>> dd <- "/home/john/temp/wrkopt/dlpkg"
>> dlname <- download.packages(cpkg, destdir=dd )[[2]]
>> cat("Downloaded ", dlname,"\n")
>> cpkg.chk <- devtools::check_built(dlname)
>> cat("Results package:",cpkg,"\n")
>> print(cpkg.chk)
>> }
>>
>> Before running this, I did
>>
>> sink("dpkgcheck.txt", split=TRUE)
>>
>> and afterwards, I did sink().
>>
>> But ... none of the check output, nor the result of the final print, show
>> up in the output file dpkgcheck.txt.
>>
>> Have I totally misunderstood sink(), or is there a nasty bug?
>>
>> I've tried running in Rstudio and in the terminal. I'm running Linux Mint
>> 18.3 Sylvia.
>>
>> Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10
>> 16:32:20 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>> john@john-j6-18 ~ $ R
>>
>> R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
>>
>>
>> J C Nash
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Saving output of check()
I got several responses to my query. Henrik's does suggest "why", but I
am rather unhappy that R has this weakness. (See below for a sort of
workaround for Linux users.)
In particular, note that the check_built() function DOES return an object,
but it does NOT print().
In fact, putting alldep <- "embryogrowth" gives a result file
> Check the dependent packages
> Downloaded /home/john/temp/wrkopt/dlpkg/embryogrowth_7.4.tar.gz
> Results package: embryogrowth
>
while the bottom of the terminal file gives
> * checking data for non-ASCII characters ... OK
> * checking data for ASCII and uncompressed saves ... OK
> * checking examples ... OK
> * DONE
>
> Status: OK
>
> Results package: embryogrowth
> R CMD check results
> 0 errors | 0 warnings | 0 notes
>
>>
>> sink()
>>
Now the object cpkg.chk is still present, so I continued the exercise (terminal
copy here)
>
>> ls()
> [1] "alldep" "cpkg" "cpkg.chk" "dd" "dlname" "ii" "nall"
>
>> sink("sinktest2.txt", split=TRUE)
>> cpkg.chk
> R CMD check results
> 0 errors | 0 warnings | 0 notes
>
>> print(cpkg.chk)
> R CMD check results
> 0 errors | 0 warnings | 0 notes
>
>> cat("note the above use just the object name as well as print()\n")
> note the above use just the object name as well as print()
>> sink()
>>
but the file sinktest2.txt is just
>
> note the above use just the object name as well as print()
Perhaps this isn't a bug, but it rather smells like one, especially the
failure to show the cpkg.chk.
Workaround for Linux: Run things via
R |& tee -a myteeoutput.txt
This will keep all the output (sink not needed). But it isn't quite as nice
for keeping the data.
I've also not managed to find a way to get the information out of the cpkg.chk
object. If someone knows how to do that, it would help.
Best, JN
On 2018-04-11 03:24 PM, Henrik Bengtsson wrote:
> R CMD check, which is used internally runs checks in standalone
> background R processes. Output from these is not capturable/sinkable
> by the master R process. The gist of what's happening is:
>
>> sink("output.log")
>> system("echo hello") ## not sinked/captured
> hello
>> sink()
>> readLines("output.log")
> character(0)
>
> /Henrik
>
> On Wed, Apr 11, 2018 at 11:05 AM, J C Nash wrote:
>> Hi,
>>
>> In trying to test that an upgrade to my optimx package does not break other
>> packages, I wanted to loop over a list of all such packages in alldep, with
>> nall the length of this list.
>>
>> cat("Check the dependent packages\n")
>> for (ii in 1:nall){
>> cpkg <- alldep[ii]
>> dd <- "/home/john/temp/wrkopt/dlpkg"
>> dlname <- download.packages(cpkg, destdir=dd )[[2]]
>> cat("Downloaded ", dlname,"\n")
>> cpkg.chk <- devtools::check_built(dlname)
>> cat("Results package:",cpkg,"\n")
>> print(cpkg.chk)
>> }
>>
>> Before running this, I did
>>
>> sink("dpkgcheck.txt", split=TRUE)
>>
>> and afterwards, I did sink().
>>
>> But ... none of the check output, nor the result of the final print, show
>> up in the output file dpkgcheck.txt.
>>
>> Have I totally misunderstood sink(), or is there a nasty bug?
>>
>> I've tried running in Rstudio and in the terminal. I'm running Linux Mint
>> 18.3 Sylvia.
>>
>> Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10
>> 16:32:20 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>> john@john-j6-18 ~ $ R
>>
>> R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
>>
>>
>> J C Nash
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Saving output of check()
R CMD check, which is used internally runs checks in standalone
background R processes. Output from these is not capturable/sinkable
by the master R process. The gist of what's happening is:
> sink("output.log")
> system("echo hello") ## not sinked/captured
hello
> sink()
> readLines("output.log")
character(0)
/Henrik
On Wed, Apr 11, 2018 at 11:05 AM, J C Nash wrote:
> Hi,
>
> In trying to test that an upgrade to my optimx package does not break other
> packages, I wanted to loop over a list of all such packages in alldep, with
> nall the length of this list.
>
> cat("Check the dependent packages\n")
> for (ii in 1:nall){
> cpkg <- alldep[ii]
> dd <- "/home/john/temp/wrkopt/dlpkg"
> dlname <- download.packages(cpkg, destdir=dd )[[2]]
> cat("Downloaded ", dlname,"\n")
> cpkg.chk <- devtools::check_built(dlname)
> cat("Results package:",cpkg,"\n")
> print(cpkg.chk)
> }
>
> Before running this, I did
>
> sink("dpkgcheck.txt", split=TRUE)
>
> and afterwards, I did sink().
>
> But ... none of the check output, nor the result of the final print, show
> up in the output file dpkgcheck.txt.
>
> Have I totally misunderstood sink(), or is there a nasty bug?
>
> I've tried running in Rstudio and in the terminal. I'm running Linux Mint
> 18.3 Sylvia.
>
> Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10 16:32:20
> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
> john@john-j6-18 ~ $ R
>
> R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
>
>
> J C Nash
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Saving output of check()
Hi,
Not really an answer but I only recently discovered devtools::revdep(), which
automates checking reverse dependencies.
Georgi Boshnakov
From: R-package-devel [r-package-devel-boun...@r-project.org] on behalf of J C
Nash [profjcn...@gmail.com]
Sent: 11 April 2018 19:05
To: List r-package-devel
Subject: [R-pkg-devel] Saving output of check()
Hi,
In trying to test that an upgrade to my optimx package does not break other
packages, I wanted to loop over a list of all such packages in alldep, with
nall the length of this list.
cat("Check the dependent packages\n")
for (ii in 1:nall){
cpkg <- alldep[ii]
dd <- "/home/john/temp/wrkopt/dlpkg"
dlname <- download.packages(cpkg, destdir=dd )[[2]]
cat("Downloaded ", dlname,"\n")
cpkg.chk <- devtools::check_built(dlname)
cat("Results package:",cpkg,"\n")
print(cpkg.chk)
}
Before running this, I did
sink("dpkgcheck.txt", split=TRUE)
and afterwards, I did sink().
But ... none of the check output, nor the result of the final print, show
up in the output file dpkgcheck.txt.
Have I totally misunderstood sink(), or is there a nasty bug?
I've tried running in Rstudio and in the terminal. I'm running Linux Mint
18.3 Sylvia.
Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10 16:32:20
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
john@john-j6-18 ~ $ R
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
J C Nash
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Saving output of check()
Hi,
In trying to test that an upgrade to my optimx package does not break other
packages, I wanted to loop over a list of all such packages in alldep, with
nall the length of this list.
cat("Check the dependent packages\n")
for (ii in 1:nall){
cpkg <- alldep[ii]
dd <- "/home/john/temp/wrkopt/dlpkg"
dlname <- download.packages(cpkg, destdir=dd )[[2]]
cat("Downloaded ", dlname,"\n")
cpkg.chk <- devtools::check_built(dlname)
cat("Results package:",cpkg,"\n")
print(cpkg.chk)
}
Before running this, I did
sink("dpkgcheck.txt", split=TRUE)
and afterwards, I did sink().
But ... none of the check output, nor the result of the final print, show
up in the output file dpkgcheck.txt.
Have I totally misunderstood sink(), or is there a nasty bug?
I've tried running in Rstudio and in the terminal. I'm running Linux Mint
18.3 Sylvia.
Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10 16:32:20
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
john@john-j6-18 ~ $ R
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
J C Nash
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
