[R-pkg-devel] nparACT package: "working directory was changed to...resetting"
Dear Community, For Fedora my package now gives a warning message when running the example: "Warning: working directory was changed to '/data/gannet/ripley/R/packages/tests-clang/nparACT.Rcheck/sleepstudy_example', resetting" I do not really know how to approach/solve this, what has recently been changed in R devel so this error message started appearing? The full message can be seen here: https://CRAN.R-project.org/web/checks/check_results_nparACT.html Any help is appreciated and rewarded with gratitude. Best, Christine [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] nparACT package: "working directory was changed to...resetting"
Hi Duncan,
Thanks a lot! Good to see that you had a similar idea, I did just that...in my
example it looks like this, however, that does not help, i.e. that is the code
that is associated with the warning…
data(sleepstudy)
wd <- getwd()
name <- "sleepstudy_example"
newdir <- paste(wd,name, sep="/")
if (dir.exists(newdir)){
setwd(newdir)
write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE, col.names =
FALSE)
r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)
} else {
dir.create(newdir)
setwd(newdir)
write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE, col.names =
FALSE)
r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)
}
setwd(wd)
}
Best,
Christine
-Ursprüngliche Nachricht-
Von: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Gesendet: Dienstag, 19. Dezember 2017 16:19
An: Blume Christine; r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] nparACT package: "working directory was changed
to...resetting"
On 19/12/2017 9:42 AM, Blume Christine wrote:
> Dear Community,
>
>
>
> For Fedora my package now gives a warning message when running the example:
>
>
>
> "Warning: working directory was changed to
> '/data/gannet/ripley/R/packages/tests-clang/nparACT.Rcheck/sleepstudy_example',
> resetting"
>
>
>
> I do not really know how to approach/solve this, what has recently been
> changed in R devel so this error message started appearing?
Previously you were allowed to change directory in an example. Now you're not.
This makes sense: the user might not want to change the working directory.
To fix this, just save the old directory, and restore it at the end of your
example. For example,
olddir <- setwd(tempdir())
# Run the rest of the example code here
setwd(olddir)
Duncan Murdoch
>
>
>
> The full message can be seen here:
> https://CRAN.R-project.org/web/checks/check_results_nparACT.html
>
>
>
> Any help is appreciated and rewarded with gratitude.
>
>
>
> Best,
>
>
>
> Christine
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing
> list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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Re: [R-pkg-devel] nparACT package: "working directory was changed to...resetting"
Actually, the report I received refers to the old 0.7 version…for whatever
reason? The version I had submitted was 0.8 in which I had corrected this.
Well, let’s see…
Another issue seems to be that the text file the example is supposed to read in
is not read (properly) using Debian:
Warning in is.na(data$activity) :
is.na() applied to non-(list or vector) of type 'NULL'
Error in 1:a : argument of length 0
I am reading in a text file with a numeric column (data$activity) and date or
datetime (which is then converted using as.POSIXct. Subsequently, I check if
there are NAs…
Any ideas what might be happening here?
Best,
Christine
-Ursprüngliche Nachricht-
Von: Iñaki Úcar [mailto:i.uca...@gmail.com]
Gesendet: Dienstag, 19. Dezember 2017 16:48
An: Blume Christine
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] nparACT package: "working directory was changed
to...resetting"
2017-12-19 16:27 GMT+01:00 Blume Christine
mailto:christine.bl...@sbg.ac.at>>:
> Hi Duncan,
>
> Thanks a lot! Good to see that you had a similar idea, I did just that...in
> my example it looks like this, however, that does not help, i.e. that is the
> code that is associated with the warning…
>
> data(sleepstudy)
>
> wd <- getwd()
>
> name <- "sleepstudy_example"
>
> newdir <- paste(wd,name, sep="/")
>
> if (dir.exists(newdir)){
>
> setwd(newdir)
>
> write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE, col.names =
> FALSE)
>
> r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)
>
> } else {
>
> dir.create(newdir)
>
> setwd(newdir)
>
> write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE, col.names =
> FALSE)
>
> r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)
>
> }
>
> setwd(wd)
>
> }
I see:
$ wget https://cran.r-project.org/src/contrib/nparACT_0.7.tar.gz
$ tar xf nparACT_0.7.tar.gz
$ grep -r setwd nparACT
nparACT/man/nparACT_flex_loop.Rd:setwd(newdir)
nparACT/man/nparACT_base_loop.Rd:setwd(newdir)
so two examples don't restore the wd as Duncan was pointing out.
Iñaki
>
>
>
> Best,
>
> Christine
>
>
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[R-pkg-devel] Debian: example file is no longer read correctly
Dear all,
I guess I need your help again. With debian my package (nparACT) gives an error
message that seems to be related to loading the data:
Warning in is.na(data$activity) :
is.na() applied to non-(list or vector) of type 'NULL'
Error in 1:a : argument of length 0
Although I have set up a virtual machine to test the package using the R devel
version with Linux (Debian), it gives me a hard time to find out what is wrong
since I do not manage to install packages using the devel version...
Does anyone know what has changed so this text file is not read in any longer?
The code for reading in the text file is:
data <- read.table(paste(path,name, sep="/"), header = F)
if (is.data.frame(data)==F){
data = as.data.frame(data)
}
if(ncol(data) == 2){
data[,1] <- as.POSIXct(data[,1])
data[,2] <- as.numeric(as.character(data[,2]))
names(data)[1] <- "time"
names(data)[2] <- "activity"
}
if(ncol(data) == 3){
names(data)[1] <- "date"
names(data)[2] <- "time"
names(data)[3] <- "activity"
data$date <- NULL
data$time <- as.POSIXct(data$time, format="%H:%M:%S")
data$activity <- as.numeric(as.character(data$activity))
}
Or can someone tell me how to install the package using R devel on Linux?
Thanks a lot!
Christine
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Re: [R-pkg-devel] Debian: example file is no longer read correctly
Dear all,
Thanks a lot for all your suggestions, which I was happy to include. All my
coding skills are self-taught so I am especially thankful for suggestions on
how to improve the code regarding defensiveness etc..
I have also followed Iñaki's excellent suggestion and checked the package with
the latest changes to the example (to circumvent the path-setting problems)
using rhub using different platforms.
I have submitted the version with the corrections again earlier and it is on
its way to CRAN now.
Thanks again,
Christine
-Ursprüngliche Nachricht-
Von: Georgi Boshnakov [mailto:georgi.boshna...@manchester.ac.uk]
Gesendet: Mittwoch, 20. Dezember 2017 14:49
An: Göran Broström; r-package-devel@r-project.org; Blume Christine
Betreff: RE: [R-pkg-devel] Debian: example file is no longer read correctly
The package on CRAN doesn't use tempdir() to change directories.
Given that the error occurs on some linux-es only, it may be worth a try to
submit the package and see if these errors will resurface.
It is difficult to debug errors on systems you don't have but some cleanup of
your code might help your users and you.
In particular, write more defensively. For example, in your function (see a
copy further bbelow) you may consider if it is fine to convert each file to a
data.frame. Even if this is successful, the data frame may not be what you
expect.
One good idea is to write exhaustive checks.
The check for nofiles > 0 was already suggested, another suggestion is after
the signature below.
Kind regards,
Georgi Boshnakov
The chunk:
=
if (ncol(data) == 2) {
...
}
if (ncol(data) == 3) {
...
}
==
can be made more robust by simply adding an 'else' (note also the else if) to
cover for a condition that "cannot" happen.
=
if (ncol(data) == 2) {
...
} else if (ncol(data) == 3) {
...
} else {
stop(""I thought that this can never happen!")
}
==
=
nparACT_flex_loop()
function (path, SR, cutoff = 1, minutes, plot = T, fulldays = T) {
files <- list.files(path)
fileext <- file_ext(files[1])
nofiles <- length(files)
bin_hr <- 60
nparACT_result <- matrix(NA, nofiles, 9)
nparACT_result <- as.data.frame(nparACT_result)
colnames(nparACT_result) <- c("IS", "IV", "RA", "L5", "L5_starttime",
"M10", "M10_starttime", "Lflex", "Lflex_starttime")
matrix_hraverage <- matrix(NA, nofiles, 24)
for (zz in 1:nofiles) {
name <- files[zz]
if (fileext == "txt") {
data <- read.table(paste(path, name, sep = "/"),
header = F)
}
else {
data <- read.csv(paste(path, name, sep = "/"), header = F)
}
if (is.data.frame(data) == F) {
data = as.data.frame(data)
}
if (ncol(data) == 2) {
data[, 1] <- as.POSIXct(data[, 1])
data[, 2] <- as.numeric(as.character(data[, 2]))
names(data)[1] <- "time"
names(data)[2] <- "activity"
}
if (ncol(data) == 3) {
names(data)[1] <- "date"
names(data)[2] <- "time"
names(data)[3] <- "activity"
data$date <- NULL
data$time <- as.POSIXct(data$time, format = "%H:%M:%S")
data$activity <- as.numeric(as.character(data$activity))
}
if (any(is.na(data$activity)) == TRUE)
stop("Please check your data! It must not contain NAs")
a <- nrow(data)
e <- SR * 60
m <- bin_hr * SR * 60
full_days <- floor(a/(e * bin_hr * 24))
if (fulldays == T) {
data <- data[1:(e * bin_hr * 24 * full_days), ]
}
a <- nrow(data)
b <- floor(a/(SR * 60))
nparACT_auxfunctions1$nparACT_filt(data, a, cutoff)
if (SR != 1/60) {
data_min <- nparACT_auxfunctions1$nparACT_data_min(b,
SR, data)
}
else {
data_min <- data$activity
}
data_hrs <- nparACT_auxfunctions1$nparACT_data_hrs(data,
a, m)
result_ISIV <- nparACT_ISIVfunctions$nparACT_ISIV(data_hrs,
bin_hr)
IS <- result_ISIV[1]
IV <- result_ISIV[2]
nparACT_result[zz, 1] <- IS
nparACT_result[zz, 2] <- IV
minaverage <- nparACT_auxfunctions1$nparACT_minaverage(a,
data_min)
if (plot == T) {
hraverage_sorted <-
nparACT_auxfunctions1$nparACT_hraverage_GA
Re: [R-pkg-devel] File name error
Hi Cathy,
I also had troubles with debian (Fedora only gave warnings) and no problems
with other systems. Mine was related to me writing a file (or rather trying to
write) in a working directory other than tempdir (can be retrieved by
tempdir()). I now write it to tempdir and then set the old working directory
again at the end of the example. Perhaps that is somehow helpful for your case
too?
I can highly recommend to test your tar.gz file with the check() function of
the rhub package. You can for example run check("pathtoyourpackage", platform =
"debian-gcc-devel") or
check_for_cran("pathtoyourpackage", platform = "debian-gcc-devel"), i.e. test
your package on debian without troubles.
Best,
Christine
-Ursprüngliche Nachricht-
Von: R-package-devel [mailto:r-package-devel-boun...@r-project.org] Im Auftrag
von Cathy Lee Gierke
Gesendet: Donnerstag, 21. Dezember 2017 07:15
An: R Package Development
Betreff: [R-pkg-devel] File name error
I am getting the following error from the auto-checks when trying to submit a
package to CRAN:
r-devel-linux-x86_64-debian-gcc
3.0.0.2 3.63 56.71 60.34 ERROR
Error in pdf(file = fileName4, width = 8, height = 10) :
cannot open file
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CATkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-51-46CAToutput.pdf'
Since this works for ALL other flavors, I am assuming it may be some file name
restrictions unique to debian-gcc??? I can't think what else would cause it to
fail only in the OS.
debian doesn't like "--"?
Cathy Lee Gierke
*“Darkness cannot drive out darkness: only light can do that. Hate cannot drive
out hate: only love can do that.” * *“The arc of the moral universe is long,
but it bends towards justice.”* *“Nothing in the world is more dangerous than
sincere ignorance and conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.” *
*“Forgiveness is not an occasional act, it is a constant attitude.” *
*“Injustice anywhere is a threat to justice everywhere.” *
― Martin Luther King Jr.
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[R-pkg-devel] ERROR (re)building vignettes
Dear community, When building my package 'SleepCycles' using devtools::check, devtools::check_win_devel, and devtools::check_rhub, I do not get warnings, errors, or notes. Nevertheless, there seems to be an error when building the vignettes eventually (https://cran-archive.r-project.org/web/checks/2021/2021-09-06_check_results_SleepCycles.html), which I did not notice and which led to the removal of the package. Does anyone know how to solve this? I read something about changing the vignette engine, but when I tried this, I ran into other issues. I cannot replicate the error, but simply resubmitting will most likely result in the same issue again. Best, Christine [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
