Thanks for your test result Simon, I really appreciate it. I borrowed a new laptop and found the issue is only reproducible on my machine, so there is something not in R or the package that causes this problem. I will stop chattering and try to figure out where the problem is. Thanks again for your time and help!
Cheers, Jiefei On Wed, Mar 11, 2020 at 6:22 PM Simon Urbanek <simon.urba...@r-project.org> wrote: > Jiefei, > > you did not commit all files into the example package - your example has > things like RcppExports.cpp as well as additional flags which are not in > your GH project. I suspect the issue is with the extra flags you're adding > - those don't come from R. Please make sure you can replicate the issue > with the GH package you created. > > Cheers, > Simon > > > * installing *source* package 'testPackage' ... > ** using staged installation > ** libs > > *** arch - i386 > echo "test1 is [1] 0.1522111 0.2533619 0.6591809" > test1 is [1] 0.1522111 0.2533619 0.6591809 > echo "R_HOME is C:/R/R-3.6.2" > R_HOME is C:/R/R-3.6.2 > echo "Fake library" > testPackage.dll > installing to > C:/R/R-3.6.2/library/00LOCK-testPackage/00new/testPackage/libs/i38 > 6 > > *** arch - x64 > echo "test1 is [1] 0.9271811 0.8040735 0.4739104" > test1 is [1] 0.9271811 0.8040735 0.4739104 > echo "R_HOME is C:/R/R-3.6.2" > R_HOME is C:/R/R-3.6.2 > echo "Fake library" > testPackage.dll > installing to > C:/R/R-3.6.2/library/00LOCK-testPackage/00new/testPackage/libs/x64 > > ** help > No man pages found in package 'testPackage' > *** installing help indices > ** building package indices > ** testing if installed package can be loaded from temporary location > *** arch - i386 > *** arch - x64 > ** testing if installed package can be loaded from final location > *** arch - i386 > *** arch - x64 > ** testing if installed package keeps a record of temporary installation > path > * DONE (testPackage) > Making 'packages.html' ... done > > > On 12/03/2020, at 4:33 AM, Wang Jiefei <szwj...@gmail.com> wrote: > > > > Thanks a lot for your suggestions. I see what you mean. I have removed > all > > unnecessary files and dependences on > https://github.com/Jiefei-Wang/example, > > but still no luck. I've tried to install the package as a user, not > admin, > > but I got the same error. Also, I apologize for spamming the mail list. I > > will keep my reply as neat as possible. > > > > Martin has suggested checking the encoding of the file and locale in the > > session info, so here is this missing information: The makefile is > encoded > > in UTF-8, and the locale is: > > > > [1] LC_COLLATE=English_United States.1252 > > [2] LC_CTYPE=English_United States.1252 > > [3] LC_MONETARY=English_United States.1252 > > [4] LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > That is where I am stuck, any help would be appreciated. > > > > Best, > > Jiefei > > > > > > > > On Wed, Mar 11, 2020 at 9:56 AM Tomas Kalibera <tomas.kalib...@gmail.com > > > > wrote: > > > >> On 3/11/20 2:26 PM, Wang Jiefei wrote: > >> > >> Thanks, Tomas. I took your suggestion and change the make file to > >> > >> test1:=$(shell $(R_HOME)/bin/R --slave -e 'runif(3)') > >> > >> all: testPackage.dll > >> echo "test1 is $(test1)" > >> echo "R_HOME is $(R_HOME)" > >> > >> However, R CMD INSTALL still gives me the same error: > >> > >>> R CMD INSTALL testPackage_1.0.tar.gz* installing to library 'C:/Program > >> Files/R/R-devel/library' > >> * installing *source* package 'testPackage' ... > >> ** using staged installation > >> ** libs > >> > >> *** arch - i386 > >> The filename, directory name, or volume label syntax is incorrect. > >> c:/Rtools/mingw_32/bin/g++ -std=gnu++11 > -I"C:/PROGRA~1/R/R-devel/include" > >> -DNDEBUG -I'C:/Program Files/R/R-devel/library/Rcpp/include' > >> -I"C:/projects/BUILD/R-source-win32/extsoft/include" -O2 -Wall > >> -mfpmath=sse -msse2 -c RcppExports.cpp -o RcppExports.o > >> c:/Rtools/mingw_32/bin/g++ -std=gnu++11 > -I"C:/PROGRA~1/R/R-devel/include" > >> -DNDEBUG -I'C:/Program Files/R/R-devel/library/Rcpp/include' > >> -I"C:/projects/BUILD/R-source-win32/extsoft/include" -O2 -Wall > >> -mfpmath=sse -msse2 -c example.cpp -o example.o > >> c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o > >> testPackage.dll tmp.def RcppExports.o example.o > >> -LC:/projects/BUILD/R-source-win32/extsoft/lib/i386 > >> -LC:/projects/BUILD/R-source-win32/extsoft/lib > >> -LC:/PROGRA~1/R/R-devel/bin/i386 -lR > >> echo "test1 is " > >> test1 is > >> echo "R_HOME is C:/PROGRA~1/R/R-devel" > >> installing to C:/Program > >> Files/R/R-devel/library/00LOCK-testPackage/00new/testPackage/libs/i386 > >> > >> > >> I have no idea how to make the example even more minimal for there is > >> literally nothing in the package now. Like you said if R just sets > R_HOME > >> and runs "make", I do not understand why it cannot find R in this case > for > >> R_HOME seems correct to me. I think there are some other things behind R > >> CMD INSTALL but my poor knowledge does not allow me to see them...Any > help > >> will be appreciated. > >> > >> Please lets not spam the whole list with this any more - this is also > why > >> I didn't add R-devel to cc originally. The makefile may be minimal, but > the > >> example package is not - you have Rcpp dependency there, two C source > >> files, some R Studio specific thing (an .Rproj file at least). Maybe it > is > >> not related, but if you want other to help you, it would be nice to > spend > >> some of your time reducing it anyway. > >> > >> That test1 is empty means that executing R has failed. You need to find > >> out why. > >> > >> I see that you are installing into C:/Program Files/R/R-devel/library. > >> Normally that directory should not be writeable. Are you running this as > >> Administrator? In principle this could be related, but better to find > out > >> directly why executing R is failing. > >> > >> Best > >> Tomas > >> > >> > >> > >> > >> Best, > >> Jiefei > >> > >> > >> On Wed, Mar 11, 2020 at 8:57 AM Tomas Kalibera < > tomas.kalib...@gmail.com> > >> wrote: > >> > >>> > >>> Thanks, Jiefei, unfortunately your example does not work on my system, > >>> and also it is far from minimal. The error message you are getting is > from > >>> Windows and could be caused for example by accidental quoting of the > path > >>> using single quotes. > >>> > >>> Issues with RStudio or devtools would have to be discussed in their > >>> mailing lists/with their authors, but my guess is that the problem is > in > >>> your local configuration, and after all you need it to work with the > base R > >>> CMD INSTALL anyway. There is not much wrong R could do here, it just > sets > >>> R_HOME and runs "make". > >>> > >>> For example this works for me, but some closer alternations of your > code > >>> work as well: > >>> > >>> test1 := $(shell $(R_HOME)/bin/R --slave -e 'runif(3)') > >>> all: > >>> echo "test1 is $(test1)" > >>> echo "R_HOME is $(R_HOME)" > >>> > >>> I would recommend that you try to narrow down your example so that it > is > >>> really minimal. Use R_HOME, not hard-coded paths, as that is what you > would > >>> use in reality anyway. Print R_HOME and check it is valid. If the > problem > >>> persists, find out why it works when invoked from the command line but > not > >>> from R CMD INSTALL. > >>> > >>> Best > >>> Tomas > >>> > >>> On 3/10/20 10:15 AM, Wang Jiefei wrote: > >>> > >>> Oops, I think both of us forget to cite the r-devel channel. > >>> > >>> Best, > >>> Jiefei > >>> > >>> On Tue, Mar 10, 2020 at 5:13 AM Wang Jiefei <szwj...@gmail.com> wrote: > >>> > >>>> Thanks for your quick response, Tomas. > >>>> > >>>> Yes, this is a path issue, I think the problem is related to R, not > the > >>>> Rtools make. I built an example package for reproducing the problem: > >>>> https://github.com/Jiefei-Wang/example > >>>> > >>>> Here is the version of my R and Rtools: > >>>> The release R version: > >>>> R version 3.6.2 (2019-12-12) > >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) > >>>> Running under: Windows 10 x64 (build 18362) > >>>> > >>>> The devel R version: > >>>> R Under development (unstable) (2020-03-09 r77919) > >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) > >>>> Running under: Windows 10 x64 (build 18362) > >>>> > >>>> Rtools version 3.5.0.4 > >>>> > >>>> Things become interesting after I did more tests. I originally thought > >>>> this might be only related to the devel R, but it seems like the > released > >>>> version is also affected. Here is a summary of my test results using > the > >>>> example package: > >>>> > >>>> 1. command-line Rtools make: Success > >>>> 2. command-line R CMD INSTALL: Failed on both R3.6.2 and R4.0 > >>>> 3. Rstudio install button: Success on R3.6.2 but failed on R4.0 > >>>> 4. Rstudio running devtool::install: Success on both > >>>> > >>>> Now the problem becomes more intricate. I have no idea which one goes > >>>> wrong. Here are the details of my test results, I hope it can be > helpful: > >>>> > >>>> *Command line:* > >>>> 1. "C:\Rtools\mingw_64\bin\mingw32-make.exe" -f > >>>> example-master/src/Makevars > >>>> test1 is [1] 0.2039269 0.1454402 0.1578401 > >>>> test2 is [1] 0.1919521 0.9257183 0.2130247 > >>>> test3 is [1] 0.06255174 0.27555363 0.72737111 > >>>> mingw32-make: *** No targets. Stop. > >>>> > >>>> 2. "C:\Program Files\R\R-3.6.2\bin\R" CMD INSTALL > testPackage_1.0.tar.gz > >>>> *** arch - x64 > >>>> test1 is [1] 0.1584299 0.9338829 0.9528810 > >>>> The filename, directory name, or volume label syntax is incorrect. > >>>> test2 is > >>>> The filename, directory name, or volume label syntax is incorrect. > >>>> test3 is > >>>> > >>>> 3. "C:\Program Files\R\R-devel\bin\R" CMD INSTALL > >>>> testPackage_1.0.tar.gz > >>>> *** arch - x64 > >>>> test1 is [1] 0.2668522 0.9246174 0.0184601 > >>>> The filename, directory name, or volume label syntax is incorrect. > >>>> test2 is > >>>> The filename, directory name, or volume label syntax is incorrect. > >>>> test3 is > >>>> > >>>> *R studio:* > >>>> 1. R3.6: Clicking the install button > >>>> ==> Rcmd.exe INSTALL --no-multiarch --with-keep.source example-master > >>>> * installing to library 'C:/Users/wangj/Documents/R/win-library/3.6' > >>>> * installing *source* package 'testPackage' ... > >>>> ** using staged installation > >>>> ** libs > >>>> test1 is [1] 0.1583112 0.6631700 0.2265564 > >>>> test2 is [1] 0.6999799 0.5205237 0.8264029 > >>>> test3 is [1] 0.3591798 0.1767392 0.2869383 > >>>> > >>>> 2. R4.0: Clicking the install button > >>>> Rcmd.exe INSTALL --no-multiarch --with-keep.source example-master > >>>> * installing to library 'C:/Program Files/R/R-devel/library' > >>>> * installing *source* package 'testPackage' ... > >>>> ** using staged installation > >>>> ** libs > >>>> test1 is [1] 0.2091070 0.5411138 0.1051517 > >>>> The filename, directory name, or volume label syntax is incorrect. > >>>> test2 is > >>>> The filename, directory name, or volume label syntax is incorrect. > >>>> test3 is > >>>> > >>>> 3. R3.6: devtools::load_all(".") > >>>> devtools::load_all(".") > >>>> Loading testPackage > >>>> Re-compiling testPackage > >>>> - installing *source* package 'testPackage' ... (364ms) > >>>> ** using staged installation > >>>> ** libs > >>>> test1 is [1] 0.93251741 0.03975758 0.57824150 > >>>> test2 is [1] 0.8681301 0.4801464 0.9112827 > >>>> test3 is [1] 0.430470791 0.008393394 0.341484128 > >>>> test1 is [1] 0.68865768 0.05354531 0.91665539 > >>>> test2 is [1] 0.19473846 0.60293655 0.09421961 > >>>> test3 is [1] 0.90653581 0.12456034 0.09526018 > >>>> > >>>> 4. R4.0: devtools::load_all(".") > >>>> Loading testPackage > >>>> Re-compiling testPackage > >>>> ─ installing *source* package 'testPackage' ... (357ms) > >>>> ** using staged installation > >>>> ** libs > >>>> test1 is [1] 0.00545376 0.30696231 0.68752312 > >>>> test2 is [1] 0.1059506 0.7506894 0.8607918 > >>>> test3 is [1] 0.5321226 0.6985332 0.7343680 > >>>> test1 is [1] 0.7722255 0.3881171 0.5611294 > >>>> test2 is [1] 0.5443175 0.8418503 0.3479382 > >>>> test3 is [1] 0.7400557 0.3322797 0.6818899 > >>>> > >>>> > >>>> Cheers, > >>>> Jiefei > >>>> > >>>> On Tue, Mar 10, 2020 at 4:11 AM Tomas Kalibera < > tomas.kalib...@gmail.com> > >>>> wrote: > >>>> > >>>>> Hi Jiefei, > >>>>> > >>>>> thanks for your report, but I don't understand from you current > >>>>> description what the problem is. Are you saying that "make" shipped > >>>>> with > >>>>> some recent Rtools is not accepting some forms of PATHs? But, which > >>>>> Rtools then, which version of make, how do you run it? > >>>>> > >>>>> Why are you referring to "R CMD INSTALL" when none of your examples > use > >>>>> it? Is "R CMD INSTALL" necessary for reproducing the problem, cannot > >>>>> you > >>>>> just run "make" directly? > >>>>> > >>>>> Or are you reporting a bug inside R itself? (you are referring to > >>>>> specific svn revisions of R). But how could R be involved in this, is > >>>>> it > >>>>> in how it executes make? > >>>>> > >>>>> Please provide a minimal but complete reproducible example, please > >>>>> provide somehow test files that can be used. Perhaps if you try to > do > >>>>> a > >>>>> little bit of debugging on your end, it might help you to narrow down > >>>>> the problem to the point that it will be then easier to understand > it. > >>>>> For example: if the problem is in "make", it should be possible to > >>>>> trigger it directly from the command line, then you could easily try > >>>>> with different versions of make and report which ones are the > problem.. > >>>>> > >>>>> Thanks > >>>>> Tomas > >>>>> > >>>>> > >>>>> On 3/10/20 8:22 AM, Wang Jiefei wrote: > >>>>>> Hi all, > >>>>>> > >>>>>> Here is a bug(or feature?) that exists at least from R 2020-02-24 > >>>>>> r77852 to 2020-03-09 r77919 on Window. Consider this example > makefile > >>>>> in a > >>>>>> package > >>>>>> ``` > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> *test1=$(shell echo 'runif(3)'|R --vanilla --slave)test2=$(shell > echo > >>>>>> 'runif(3)'|"C:/Program Files/R/R-devel/bin/R" --vanilla > >>>>>> --slave)test3=$(shell echo 'runif(3)'|"C:/PROGRA~1/R/R-devel/bin/R" > >>>>>> --vanilla --slave)$(info test1 is $(test1))$(info test2 is > >>>>> $(test2))$(info > >>>>>> test3 is $(test3))* > >>>>>> ``` > >>>>>> > >>>>>> I have no problem running the file using GUN make or installing the > >>>>> package > >>>>>> on R 3.6, both give the same result. > >>>>>> ``` > >>>>>> *C:\Rtools\mingw_64\bin\mingw32-make.exe * > >>>>>> > >>>>>> > >>>>>> > >>>>>> *test1 is [1] 0.3427626 0.8027041 0.5611914test2 is [1] 0.9904205 > >>>>> 0.3922129 > >>>>>> 0.5970083test3 is [1] 0.3469528 0.1993838 0.8434841mingw32-make: *** > >>>>> No > >>>>>> targets. Stop.* > >>>>>> *```* > >>>>>> > >>>>>> However, on the devel version of R, it cannot recognize both the > full > >>>>> and > >>>>>> short path of R and gives an error > >>>>>> ``` > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> *test1 is [1] 0.42686376 0.84126831 0.09538047The filename, > directory > >>>>>> name, or volume label syntax is incorrect.test2 isThe filename, > >>>>> directory > >>>>>> name, or volume label syntax is incorrect.test3 is* > >>>>>> ``` > >>>>>> > >>>>>> I found this issue because my package needs to call R functions in > the > >>>>>> makefile. The code is similar to: > >>>>>> ``` > >>>>>> * myvar = $(shell echo 'runif(3)'|"${R_HOME}/bin/R" --vanilla > >>>>> --slave)* > >>>>>> ``` > >>>>>> Since *R_HOME *is set to *C:/PROGRA~1/R/R-devel/*, this will result > >>>>> in the > >>>>>> same error as I mentioned above. I do not know whether this is > >>>>> intentional. > >>>>>> If so, what is the correct way to call R function in a makefile? > >>>>>> > >>>>>> Best, > >>>>>> Jiefei > >>>>>> > >>>>>> [[alternative HTML version deleted]] > >>>>>> > >>>>>> ______________________________________________ > >>>>>> R-devel@r-project.org mailing list > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel > >>>>> > >>>>> > >>>>> > >>> > >> > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
