v4.1.0 was not submitted to CRAN, because #5987 had not been resolved.
Dear maintainer, package lightgbm_4.0.0.tar.gz does not pass the incoming checks automatically.
The logs linked from those messagges showed one issue remaining on Debian (0 on Windows).
* checking examples ... [7s/4s] NOTE
Examples with CPU time > 2.5 times elapsed time
user system elapsed ratio
lgb.restore_handle 1.206 0.085 0.128 10.08
Chose to document the issue and need for a fix in #5987, but not resubmit, to avoid annoying CRAN maintainers.
Dear maintainer, package lightgbm_4.0.0.tar.gz does not pass the incoming checks automatically.
The logs linked from those messages showed the following issues from R CMD check.
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
merge:
function(x, y, ...)
merge.eval.string:
function(env)
format:
function(x, ...)
format.eval.string:
function(eval_res, eval_err)
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking examples ... [8s/4s] NOTE
Examples with CPU time > 2.5 times elapsed time
user system elapsed ratio
lgb.restore_handle 1.819 0.128 0.165 11.8
Attempted to fix these with #5988 and resubmitted.
Reason was
Flavor: r-devel-windows-x86_64 Check: OOverall checktime, Result: NOTE Overall checktime 14 min > 10 min
but the maintainer cannot do much to reduce this, so I triggered revdep checks now. Please reply to the archival message in case the issue is not fixable easily.
Best, Uwe Ligges
This was technically not a "resubmission". We asked CRAN why the first v3.3.5 submission had been archived, and they responded with the response above... and then v3.3.5 passed all checks with no further work from LightGBM maintainers.
Archived without a response.
Submitted with the following comment.
This submission contains {lightgbm} 3.3.5
Per CRAN's policies, I am submitting it on behalf of the project's maintainer (Yu Shi), with his permission.
This submission includes patches to address the following warnings observed on the fedora and debian CRAN checks.
Found the following significant warnings: io/json11.cpp:207:47: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] io/json11.cpp:216:51: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] io/json11.cpp:225:53: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] io/json11.cpp:268:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] io/json11.cpp:272:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] io/json11.cpp:276:37: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] io/json11.cpp:381:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] io/json11.cpp:150:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Thank you very much for your time and consideration.
Accepted to CRAN
Submitted with the following comment:
This submission contains {lightgbm} 3.3.4
Per CRAN's policies, I am submitting it on behalf of the project's maintainer (Yu Shi), with his permission.
This submission includes patches to address the following warnings observed on the fedora and debian CRAN checks.
Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.
Thank you very much for your time and consideration.
Accepted to CRAN
Submitted with the following comment:
This submission contains {lightgbm} 3.3.3.
Per CRAN's policies, I am submitting on it on behalf of the project's maintainer (Yu Shi), with his permission (#5525).
This submission includes two patches:
Thank you very much for your time and consideration.
Accepted to CRAN on January 14, 2022.
In this submission, we uploaded a patch that CRAN stuff provided us via e-mail. The full text of the e-mail from CRAN:
Dear maintainers,
This concerns the CRAN packages
Cairo cepreader gpboost httpuv ipaddress lightgbm proj4 prophet
RcppCWB RcppParallel RDieHarder re2 redux rgeolocate RGtk2 tth
udunits2 unrtf
maintained by one of you:
Andreas Blaette andreas.blaette@uni-due.de: RcppCWB
David Hall david.hall.physics@gmail.com: ipaddress
Dirk Eddelbuettel edd@debian.org: RDieHarder
Fabio Sigrist fabiosigrist@gmail.com: gpboost
Friedrich Leisch Friedrich.Leisch@R-project.org: tth
Girish Palya girishji@gmail.com: re2
James Hiebert hiebert@uvic.ca: udunits2
Jari Oksanen jhoksane@gmail.com: cepreader
Kevin Ushey kevin@rstudio.com: RcppParallel
ORPHANED: RGtk2
Os Keyes ironholds@gmail.com: rgeolocate
Rich FitzJohn rich.fitzjohn@gmail.com: redux
Sean Taylor sjtz@pm.me: prophet
Simon Urbanek simon.urbanek@r-project.org: proj4
Simon Urbanek Simon.Urbanek@r-project.org: Cairo
Winston Chang winston@rstudio.com: httpuv
Yu Shi yushi2@microsoft.com: lightgbm
your packages need to be updated for R-devel/R 4.2 to work on Windows,
following the recent switch to UCRT and Rtools42.
Sorry for the group message, please feel free to respond individually
regarding your package or ask specifically about what needs to be fixed.
I've created patches for you, so please review them and fix your packages:
https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsvn.r-project.org%2FR-dev-web%2Ftrunk%2FWindowsBuilds%2Fwinutf8%2Fucrt3%2Fr_packages%2Fpatches%2FCRAN%2F&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rFGf7Y4Dvo6g1kzV%2BeAJDLGm1TUtzQsLsavElTw6H1U%3D&reserved=0
You can apply them as follows
tar xfz package_1.0.0.tar.gz
wget
https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsvn.r-project.org%2FR-dev-web%2Ftrunk%2FWindowsBuilds%2Fwinutf8%2Fucrt3%2Fr_packages%2Fpatches%2FCRAN%2Fpackage.diff&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=iyTjhoqvzj3IbQ8HGCZeh1IQl34FAGpIdVyZWkzNvO0%3D&reserved=0
patch --binary < package.diff
These patches are currently automatically applied by R-devel on Windows
at installation time, which makes most of your packages pass their
checks (as OK or NOTE), but please check your results carefully and
carefully review the patches. Usually these changes were because of
newer GCC or newer MinGW in the toolchain, but some for other reasons,
and some of them will definitely have to be improved so that the package
keeps building also for older versions of R using Rtools40. We have only
been testing the patches with UCRT (and Rtools42) on Windows.
For more information, please see
https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdeveloper.r-project.org%2FBlog%2Fpublic%2F2021%2F12%2F07%2Fupcoming-changes-in-r-4.2-on-windows%2F&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=SY77zgtbDbHvTxTgPLOoe%2Fw5OZDhXvJoxpVOoEaKoYo%3D&reserved=0
https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdeveloper.r-project.org%2FWindowsBuilds%2Fwinutf8%2Fucrt3%2Fhowto.html&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=dlVJ4nhQlmDPd56bHoVsWZuRfrUUorvOWxoUTmVDM%2Bg%3D&reserved=0
Once you add your patches/fix the issues, your package will probably
show a warning during R CMD check (as patching would be attempted to be
applied again). That's ok, at that point please let me know and I will
remove my patch from the repository of automatically applied patches.
If you end up just applying the patch as is, there is probably no need
testing on your end, but you can do so using Winbuilder, r-hub, github
actions (e.g. https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkalibera%2Fucrt3&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=msqoPzqDStlAUn%2Bb6gGevwFPD%2FaNL5dTxiNud2Sqzy8%3D&reserved=0).
If you wanted to test locally on your Windows machine and do not have a
UCRT version of R-devel yet, please uninstall your old version of
R-devel, delete the old library used with that, install a new UCRT
version of R-devel , and install Rtools42. You can keep Rtools40
installed if you need it with R 4.1 or earlier.
Currently, the new R-devel can be downloaded from
https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.r-project.org%2Fnosvn%2Fwinutf8%2Fucrt3%2Fweb%2Frdevel.html&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0hCwONzLmcW0GIXNqiOZQEIuhNA%2BjHhQvXsofs8J98o%3D&reserved=0
And Rtools42 from
https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.r-project.org%2Fnosvn%2Fwinutf8%2Fucrt3%2Fweb%2Frtools.html&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=WLWLbOyQKbaYz8gkfKz2sqoGknjIOtl1aGAhUF%2Bpylg%3D&reserved=0
If you end up testing locally, you can use R_INSTALL_TIME_PATCHES
environment variable to disable the automated patching, see the "howto"
document above. That way you could also see what the original issue was
causing.
If you wanted to find libraries to link for yourself, e.g. in a newer
version of your package, please look for "Using findLinkingOrder with
Rtools42 (tiff package example)" in the "howto" document above. I
created the patches for you manually before we finished this script, so
you may be able to create a shorter version using it, but - it's
probably not worth the effort.
If you wanted to try in a virtual machine, but did not have a license,
you can use also an automated setup of a free trial VM from
https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdeveloper.r-project.org%2FBlog%2Fpublic%2F2021%2F03%2F18%2Fvirtual-windows-machine-for-checking-r-packages&data=04%7C01%7Cyushi2%40microsoft.com%7C8e6c353d1a8842c81eeb08d9bef5d835%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637750786169848244%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=aFFQYuC9CoBwBiLgZHi8N3yUnSiHu5Xtdqb2YBiMIHQ%3D&reserved=0
(but that needs a very good and un-metered network connection to install)
Please let us know if you have any questions.
Thanks,
Tomas & Uwe
Accepted to CRAN on October 30, 2021.
CRAN completed its checks and preparation of binaries on November 6, 2021.
Submitted v3.3.1 to CRAN, with the following fixes for the issues that caused CRAN to reject v3.3.0 and archive the package:
Submitted with the following comment:
This submission contains {lightgbm} 3.3.1. Per CRAN's policies, I am submitting on it on behalf of the project's maintainer (Yu Shi), with his permission (#4715 (comment)).
{lightgbm} was removed from CRAN on October 25, 2021 due to issues detected in the gcc-ASAN and clang-ASAN checks. To the best of our knowledge, we believe this release fixes those issues. We have introduced automated testing that we believe faithfully reproduces CRAN's tests with sanitizers (#4678).
Thank you very much for your time and consideration.
Progress on the submission was tracked in #4713.
{lightgbm} was removed from CRAN entirely on October 25, 2021.
On October 12, 2021, maintainers received the following message from CRAN (ripley@stats.ox.ac.uk):
Dear maintainer,
Please see the problems shown on https://cran.r-project.org/web/checks/check_results_lightgbm.html
Please correct before 2021-10-25 to safely retain your package on CRAN.
Do remember to look at the 'Additional issues'.
The CRAN Team
We failed to produce a new submission prior to that date, so the package was removed entirely.
See #4713 for additional background and links explaining the specific failed CRAN checks.
In this submission, we attempted to switch the maintainer of the package (in the CRAN official sense) from Guolin Ke to Yu Shi. Did this by adding a note in the CRAN submission web form explaining Guolin's departure from Microsoft.
Accepted to CRAN.
Package is failing checks in the r-devel-linux-x86_64-debian-clang environment (described here). Specifically, one unit test on the use of non-ASCII feature names in Booster$dump_model() fails.
Apparently your package fails its checks in a strict Latin-1* locale, e.g. under Linux using LANG=en_US.iso88591 (see the debian-clang results).
Please correct before 2021-04-21 to safely retain your package on CRAN.
Submitted a version 3.2.1 to correct the errors noted.
Accepted to CRAN, December 8.
Submitted a fix to 3.1.0 that skips some learning-to-rank tests on 32-bit Windows.
Accepted to CRAN, November 18.
On November 21, found out that the CRAN's r-oldrel-windows-ix86+x86_64 check was failing, with an issue similar to the one faced on Solaris and fixed in #3534.
CRAN did not ask for a re-submission, but this was fixed in 3.1.1.
This package was submitted with the following information in the "optional comments" box.
Hello,
I'm submitting {lightgbm} 3.1.0 on behalf of the maintainer, Guolin Ke. I am a co-author on the package, and he has asked me to handle this submission. We saw in https://cran.r-project.org/web/packages/policies.html#Submission that this is permitted.
{lightgbm} was removed from CRAN in October for issues found by valgrind checks. We have invested significant effort in addressing those issues and creating an automatic test that tries to replicate CRAN's valgrind checks: https://github.com/microsoft/LightGBM/blob/742d72f8bb051105484fd5cca11620493ffb0b2b/.github/workflows/r_valgrind.yml.
We see two warnings from valgrind that we believe are not problematic.
==2063== Conditional jump or move depends on uninitialised value(s)
==2063== at 0x49CF138: gregexpr_Regexc (grep.c:2439)
==2063== by 0x49D1F13: do_regexpr (grep.c:3100)
==2063== by 0x49A0058: bcEval (eval.c:7121)
==2063== by 0x498B67F: Rf_eval (eval.c:727)
==2063== by 0x498E414: R_execClosure (eval.c:1895)
==2063== by 0x498E0C7: Rf_applyClosure (eval.c:1821)
==2063== by 0x499FC8C: bcEval (eval.c:7089)
==2063== by 0x498B67F: Rf_eval (eval.c:727)
==2063== by 0x498B1CB: forcePromise (eval.c:555)
==2063== by 0x49963AB: FORCE_PROMISE (eval.c:5142)
==2063== by 0x4996566: getvar (eval.c:5183)
==2063== by 0x499D1A5: bcEval (eval.c:6873)
==2063== Uninitialised value was created by a stack allocation
==2063== at 0x49CEC37: gregexpr_Regexc (grep.c:2369)
This seems to be related to R itself and not any code in {lightgbm}.
==2063== 336 bytes in 1 blocks are possibly lost in loss record 153 of 2,709
==2063== at 0x483DD99: calloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==2063== by 0x40149CA: allocate_dtv (dl-tls.c:286)
==2063== by 0x40149CA: _dl_allocate_tls (dl-tls.c:532)
==2063== by 0x5702322: allocate_stack (allocatestack.c:622)
==2063== by 0x5702322: pthread_create@@GLIBC_2.2.5 (pthread_create.c:660)
==2063== by 0x56D0DDA: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==2063== by 0x56C88E0: GOMP_parallel (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==2063== by 0x1544D29C: LGBM_DatasetCreateFromCSC (c_api.cpp:1286)
==2063== by 0x1546F980: LGBM_DatasetCreateFromCSC_R (lightgbm_R.cpp:91)
==2063== by 0x4941E2F: R_doDotCall (dotcode.c:634)
==2063== by 0x494CCC6: do_dotcall (dotcode.c:1281)
==2063== by 0x499FB01: bcEval (eval.c:7078)
==2063== by 0x498B67F: Rf_eval (eval.c:727)
==2063== by 0x498E414: R_execClosure (eval.c:1895)
We believe this is a false positive, and related to a misunderstanding between valgrind and openmp (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=36298).
We have also added automated tests with ASAN/UBSAN to our testing setup, and have checked the package on Solaris 10 and found no issues.
Thanks for your time and consideration.
First response was a message talking about failing checks on 3.0.0.
package lightgbm_3.0.0.2.tar.gz has been auto-processed.
The auto-check found additional issues for the last version released on CRAN:
gcc-UBSAN <link>
valgrind <link>
CRAN incoming checks do not test for these additional issues and you will need an appropriately instrumented build of R to reproduce these.
Hence please reply-all and explain: Have these been fixed?
Please correct before 2020-10-05 to safely retain your package on CRAN.
There is still a valgrind error. This did not happen when tested on
submission, but the tests did run until timeout at 4 hours. When you
write illegally, corruption is common.
Illegal writes are serious errors.
Then in later responses to email correspondence with CRAN, CRAN expressed frustration with the number of failed submission and banned this package from new submissions for a month.
The content of that frustrated message was regrettable and it does not need to be preserved forever in this file.
The 3.0.0.x series is officially not making it to CRAN. We will wait until November, and try again.
Detailed plan about what will be tried before November 2020 to increase the likelihood of success for that package: #3338 (comment).
Thanks, we see:
Still lots of alignment errors, such as
lightgbm.Rcheck/tests/testthat.Rout:io/dataset_loader.cpp:340:59:
runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const value_type', which requires 4 byte alignment
lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/stl_vector.h:1198:21:
runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const int', which requires 4 byte alignment lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/vector.tcc:449:28:runtime
error: reference binding to misaligned address 0x7f51fefad81e for type 'const type', which requires 4 byte alignment
lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/move.h:77:36:
runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const int', which requires 4 byte alignment
lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/alloc_traits.h:512:17:
runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const type', which requires 4 byte alignment
Please fix and resubmit.
Ok, these are the notes from the UBSAN tests. Was able to reproduce them with #3338 (comment), and they were fixed in #3415.
Struggling to replicate the valgrind result (running R CMD check --use-valgrind returns no issues), so trying submission again. Hoping that the fixes for mis-alignment fix the other errors too.
Failing pre-checks.
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Guolin Ke <guolin.ke@microsoft.com>’
Insufficient package version (submitted: 3.0.0, existing: 3.0.0)
Days since last update: 4
Did not think the version needed to be incremented if submitting a package in response to CRAN saying "you are failing checks and will be kicked off if you don't fix it", but I guess you do!
This can be fixed by just re-submitting but with the version changed from 3.0.0 to 3.0.0.1.
Accepted to CRAN!
Please correct the problems below before 2020-10-05 to safely retain your package on CRAN:
checking installed package size ... NOTE
installed size is 49.7Mb
sub-directories of 1Mb or more:
libs 49.1Mb
"network/socket_wrapper.hpp", line 30: Error: Could not open include file<ifaddrs.h>.
"network/socket_wrapper.hpp", line 216: Error: The type "ifaddrs" is incomplete.
"network/socket_wrapper.hpp", line 217: Error: The type "ifaddrs" is incomplete.
"network/socket_wrapper.hpp", line 220: Error: The type "ifaddrs" is incomplete.
"network/socket_wrapper.hpp", line 222: Error: The type "ifaddrs" is incomplete.
"network/socket_wrapper.hpp", line 214: Error: The function "getifaddrs" must have a prototype.
"network/socket_wrapper.hpp", line 228: Error: The function "freeifaddrs" must have a prototype.
"network/linkers_socket.cpp", line 76: Warning: A non-POD object of type "std::chrono::duration<double, std::ratio<1, 1000>>" passed as a variable argument to function "static LightGBM::Log::Info(const char*, ...)".
7 Error(s) and 1 Warning(s) detected.
*** Error code 2
make: Fatal error: Command failed for target `network/linkers_socket.o'
Current working directory /tmp/RtmpNfaavG/R.INSTALL40a84f70130a/lightgbm/src
ERROR: compilation failed for package ‘lightgbm’
* removing ‘/home/ripley/R/Lib32/lightgbm’
Added a patch that psutil has used to fix missing ifaddrs.h on Solaris 10: #629 (comment).
Thanks, if the running time is the only reason to wrap the examples in \donttest, please replace \donttest by \donttest (\donttest examples are not executed in the CRAN checks).
Please replace cat() by message() or warning() in your functions (except for print() and summary() functions). Messages and warnings can be suppressed if needed.
Missing Rd-tags: lightgbm/man/dimnames.lgb.Dataset.Rd: \value lightgbm/man/lgb.Dataset.construct.Rd: \value lightgbm/man/lgb.prepare.Rd: \value ...
Please add the tag and explain in detail the returned objects.
Responded to CRAN with the following:
All examples have been wrapped with \donttest as requested. We have replied to Swetlana Herbrandt asking for clarification on the donttest news item in the R 4.0.2 changelog (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html).
All uses of cat() have been replaced with print(). We chose print() over message() because it's important that they be written to stdout alongside all the other logs coming from the library's C++ code. message() and warning() write to stderr.
All exported objects now have \value{} statements in their documentation files in man/.
We also replied directly to CRAN's feedback email
Swetlana,
Thank you for your comments. I've just created a new submission that I believe addresses them.
Can you help us understand something? In your message you said "\donttest examples are not executed in the CRAN checks)", but in https://cran.r-project.org/doc/manuals/r-devel/NEWS.html we see the following:
"
R CMD check --as-crannow runs \donttest examples (which are run by example()) instead of instructing the tester to do so. This can be temporarily circumvented during development by setting environment variable_R_CHECK_DONTTEST_EXAMPLES_to a false value."
Could you help us understand how both of those statements can be true?
-
Please write references in the description of the DESCRIPTION file in the form
- authors (year) doi:...
- authors (year) arXiv:...
- authors (year, ISBN:...)
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if those are not available: authors (year) https:... with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for auto-linking.
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(If you want to add a title as well please put it in quotes: "Title")
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\donttest{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \donttest{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please unwrap the examples if they are executable in < 5 sec, or replace \donttest{} with \donttest{}.
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Please do not modify the global environment (e.g. by using <<-) in your functions. This is not allowed by the CRAN policies.
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Please always add all authors, contributors and copyright holders in the Authors@R field with the appropriate roles. From CRAN policies you agreed to: "The ownership of copyright and intellectual property rights of all components of the package must be clear and unambiguous (including from the authors specification in the DESCRIPTION file). Where code is copied (or derived) from the work of others (including from R itself), care must be taken that any copyright/license statements are preserved and authorship is not misrepresented." e.g.: Microsoft Corporation, Dropbox Inc. Please explain in the submission comments what you did about this issue.
Please fix and resubmit
Responded to CRAN with the following:
The paper citation has been adjusted as requested. We were using 'glmnet' as a guide on how to include the URL but maybe they are no longer in compliance with CRAN policies: https://github.com/cran/glmnet/blob/b1a4b50de01e0cd24343959d7cf86452bac17b26/DESCRIPTION
All authors from the original LightGBM paper have been added to Authors@R as "aut". We have also added Microsoft and DropBox, Inc. as "cph" (copyright holders). These roles were chosen based on the guidance in https://journal.r-project.org/archive/2012-1/RJournal_2012-1_Hornik~et~al.pdf.
lightgbm's code does use <<-, but it does not modify the global environment. The uses of <<- in R/lgb.interprete.R and R/callback.R are in functions which are called in an environment created by the lightgbm functions that call them, and this operator is used to reach one level up into the calling function's environment.
We chose to wrap our examples in \donttest{} because we found, through testing on https://builder.r-hub.io/ and in our own continuous integration environments, that their run time varies a lot between platforms, and we cannot guarantee that all examples will run in under 5 seconds. We intentionally chose \donttest{} over \donttest{} because this item in the R 4.0.0 changelog (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html) seems to indicate that \donttest will be ignored by CRAN's automated checks:
"
R CMD check --as-crannow runs \donttest examples (which are run by example()) instead of instructing the tester to do so. This can be temporarily circumvented during development by setting environment variable_R_CHECK_DONTTEST_EXAMPLES_to a false value."
We run all examples with R CMD check --as-cran --run-dontrun in our continuous integration tests on every commit to the package, so we have high confidence that they are working correctly.
Failing pre-checks.
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Debian: 2 NOTEs
* checking CRAN incoming feasibility ... NOTE Maintainer: 'Guolin Ke <guolin.ke@microsoft.com>' New submission Possibly mis-spelled words in DESCRIPTION: Guolin (13:52) Ke (13:48) LightGBM (14:20) al (13:62) et (13:59) * checking top-level files ... NOTE Non-standard files/directories found at top level: 'docs' 'lightgbm-hex-logo.png' 'lightgbm-hex-logo.svg' -
Windows: 2 NOTEs
* checking CRAN incoming feasibility ... NOTE Maintainer: 'Guolin Ke <guolin.ke@microsoft.com>' New submission Possibly mis-spelled words in DESCRIPTION: Guolin (13:52) Ke (13:48) LightGBM (14:20) al (13:62) et (13:59) * checking top-level files ... NOTE Non-standard files/directories found at top level: 'docs' 'lightgbm-hex-logo.png' 'lightgbm-hex-logo.svg'
We should tell them the misspellings note is a false positive.
For the note about included files, that is my fault. I had extra files laying around when I generated the package. I'm surprised to see docs/ in that list, since it is ignored in .Rbuildignore. I even tested that with the exact code Rbuildignore uses. For now, I added rm -r docs/ to build-cran-package.sh. We can figure out what is happening with .Rbuildignore in the future, but it shouldn't block a release.
NOTE: 3.0.0-1 was never released to CRAN. CRAN was on vacation August 14-24, 2020, and in that time version 3.0.0-1 (a release candidate) became 3.0.0.
Please only ship the CRAN template for the MIT license.
Is there some reference about the method you can add in the Description field in the form Authors (year) doi:.....?
Please fix and resubmit.
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Debian: 1 NOTE
* checking CRAN incoming feasibility ... NOTE Maintainer: ‘Guolin Ke <guolin.ke@microsoft.com>’ New submission License components with restrictions and base license permitting such: MIT + file LICENSE -
Windows: 1 NOTE
* checking CRAN incoming feasibility ... NOTE Maintainer: 'Guolin Ke <guolin.ke@microsoft.com>' New submission License components with restrictions and base license permitting such: MIT + file LICENSE
Tried updating LICENSE file to this template:
YEAR: 2016
COPYRIGHT HOLDER: Microsoft CorporationAdded a citation and link for the main paper in DESCRIPTION.
Failing pre-checks.
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Debian: 1 NOTE
* checking CRAN incoming feasibility ... NOTE Maintainer: ‘Guolin Ke <guolin.ke@microsoft.com>’ New submission License components with restrictions and base license permitting such: MIT + file LICENSE -
Windows: 1 ERROR, 1 NOTE
* checking CRAN incoming feasibility ... NOTE Maintainer: ‘Guolin Ke <guolin.ke@microsoft.com>’ New submission License components with restrictions and base license permitting such: MIT + file LICENSE ** running tests for arch 'i386' ... [9s] ERROR Running 'testthat.R' [8s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(lightgbm) Loading required package: R6 > > test_check( + package = "lightgbm" + , stop_on_failure = TRUE + , stop_on_warning = FALSE + ) -- 1. Error: predictions do not fail for integer input (@test_Predictor.R#7) -- lgb.Dataset.construct: cannot create Dataset handle Backtrace: 1. lightgbm::lgb.train(...) 2. data$construct()
The "checking CRAN incoming feasibility" NOTE can be safely ignored. It only shows up the first time you submit a package to CRAN.
So the only thing I see broken right now is the test error on 32-bit Windows. This is documented in #3187.
Failing pre-checks.
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Debian: 2 NOTEs
* checking CRAN incoming feasibility ... NOTE Maintainer: ‘Guolin Ke <guolin.ke@microsoft.com>’ New submission License components with restrictions and base license permitting such: MIT + file LICENSE Non-standard files/directories found at top level: ‘cran-comments.md’ ‘docs’ -
Windows: 1 ERROR, 2 NOTEs
* checking CRAN incoming feasibility ... NOTE Maintainer: 'Guolin Ke <guolin.ke@microsoft.com>' New submission License components with restrictions and base license permitting such: MIT + file LICENSE * checking top-level files ... NOTE Non-standard files/directories found at top level: 'cran-comments.md' 'docs' ** checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error: package 'lightgbm' is not installed for 'arch = i386' Execution halted
Seems removing Biarch field didn't work. Noticed this in the install logs:
Warning: this package has a non-empty 'configure.win' file, so building only the main architecture
Tried adding Biarch: true to DESCRIPTION to overcome this.
NOTE about non-standard files was the result of a mistake in .Rbuildignore syntax, and something strange with how cran-comments.md line in .Rbuildignore was treated. Updated .Rbuildignore and added an rm cran-comments.md to build-cran-package.sh.
Failing pre-checks.
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Debian: 1 NOTE
Possibly mis-spelled words in DESCRIPTION: LightGBM (12:88, 19:41, 20:60, 20:264) -
Windows: 1 ERROR, 1 NOTE
Possibly mis-spelled words in DESCRIPTION: LightGBM (12:88, 19:41, 20:60, 20:264) ** checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error: package 'lightgbm' is not installed for 'arch = i386' Execution halted
Thought the issue on Windows was caused by Biarch: false in DESCRIPTION. Removed Biarch field.
Thought the "misspellings" issue could be resolved by adding single quotes around LightGBM, like 'LightGBM'.