date:20210704

Re: [R-pkg-devel] R-CMD-check works locally and on github, but windows automatic checks fail

2021-07-04 Thread Duncan Murdoch

On 04/07/2021 5:26 p.m., Cyril Lagger wrote:

Hi all,

I am trying to submit our package scDiffCom (
https://github.com/CyrilLagger/scDiffCom) to CRAN. However, it does not
pass the windows automatic checks for some unclear reason to me. Any help
would be really appreciated!

Basically, the output from R-CMD-check is fine locally and for the github
actions I specified, but not for the automatic windows tests. Please see
below:

1)
no ERRORs, no WARNINGs, no NOTEs when running devtools:check() locally
(windows 10, R 4.1.0)

That's the windows release version, not devel.

2)
no ERRORs, no WARNINGs, no NOTEs when running github-actions

for windows-latest (release), macOS-latest (release), ubuntu-20.04
(release), ubuntu-20.04 (devel)

You didn't test windows-devel.

3)
1 ERROR when running devtools:check_win_devel: *Running the tests in
'tests/testthat.R' failed.* However, testthat.Rout.fail is not informative
to me, it only contains:

That's a Windows devel run.  That's what you haven't done locally.

library(testthat)
library(scDiffCom)

test_check("scDiffCom")

Loading required package: SeuratObject

4)
2 ERRORs when running devtools:check_win_release. As follows:

** running tests for arch 'i386' ... [5s] ERROR
   Running 'spelling.R' [0s]
   Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
   > library(testthat)
   > library(scDiffCom)
   >
   > test_check("scDiffCom")
   Loading required package: SeuratObject
   == Failed tests

   -- Error (test-everything.R:171:1): (code run outside of
`test_that()`) 
   Error: error in load action .__A__.1 for package RcppAnnoy:
loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow =
TRUE): Unable to load module "AnnoyAngular": bad binding access
   Backtrace:
x
 1. +-base::lapply(...) test-everything.R:171:0
 2. | \-scDiffCom:::FUN(X[[i]], ...)
 3. |   \-scDiffCom:::extract_analysis_inputs(...) test-everything.R:174:4
 4. | \-scDiffCom:::extract_seurat_inputs(...)
 5. \-base::loadNamespace(x)
 6.   +-base::namespaceImportFrom(...)
 7.   | \-base::asNamespace(ns)
 8.   \-base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]])
 9. \-methods::cacheMetaData(ns, TRUE, ns)
10.   \-methods:::.doLoadActions(where, attach)

   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
   Error: Test failures
   Execution halted
** running tests for arch 'x64' ... [5s] ERROR
   Running 'spelling.R' [0s]
   Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
   > library(testthat)
   > library(scDiffCom)
   >
   > test_check("scDiffCom")
   Loading required package: SeuratObject

---

Since I have no error locally on my machine, I don't know what I could
change for the automatic tests to work. Also, I don't understand why
the github-action for windows-latest (release) works but not
devtools:check_win_release().

You say check_win_devel() above.

By the way, I installed R devel on my machine in addition to R 4.1.0,
but it turns out I cannot test our package installation because it has
Bioconductor dependencies and "Bioconductor does not yet build and
check packages for R version 4.2" as reported here
. The exact same error
actually also occurs when I run devtools:check_rhub(). It does not
seem to be related to the failure of testthat I reported above, but I
thought it might be useful to mention it.

Yes, seems related.  If you're depending on a package that won't build, 
your tests will fail.

Perhaps you can reduce your dependence to Suggests, which will give a 
note on the failure to load, but no more.

I don't know if this is under your control, but I believe R-devel will 
not support i386.  (Or is it the last version to do so?  I forget where 
I saw the news.)

Duncan Murdoch

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] R-CMD-check works locally and on github, but windows automatic checks fail

2021-07-04 Thread Cyril Lagger

Hi all,

I am trying to submit our package scDiffCom (
https://github.com/CyrilLagger/scDiffCom) to CRAN. However, it does not
pass the windows automatic checks for some unclear reason to me. Any help
would be really appreciated!

Basically, the output from R-CMD-check is fine locally and for the github
actions I specified, but not for the automatic windows tests. Please see
below:


1)
no ERRORs, no WARNINGs, no NOTEs when running devtools:check() locally
(windows 10, R 4.1.0)

2)
no ERRORs, no WARNINGs, no NOTEs when running github-actions

for windows-latest (release), macOS-latest (release), ubuntu-20.04
(release), ubuntu-20.04 (devel)

3)
1 ERROR when running devtools:check_win_devel: *Running the tests in
'tests/testthat.R' failed.* However, testthat.Rout.fail is not informative
to me, it only contains:

> library(testthat)
> library(scDiffCom)
>
> test_check("scDiffCom")
Loading required package: SeuratObject

4)
2 ERRORs when running devtools:check_win_release. As follows:

** running tests for arch 'i386' ... [5s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(scDiffCom)
  >
  > test_check("scDiffCom")
  Loading required package: SeuratObject
  == Failed tests

  -- Error (test-everything.R:171:1): (code run outside of
`test_that()`) 
  Error: error in load action .__A__.1 for package RcppAnnoy:
loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow =
TRUE): Unable to load module "AnnoyAngular": bad binding access
  Backtrace:
   x
1. +-base::lapply(...) test-everything.R:171:0
2. | \-scDiffCom:::FUN(X[[i]], ...)
3. |   \-scDiffCom:::extract_analysis_inputs(...) test-everything.R:174:4
4. | \-scDiffCom:::extract_seurat_inputs(...)
5. \-base::loadNamespace(x)
6.   +-base::namespaceImportFrom(...)
7.   | \-base::asNamespace(ns)
8.   \-base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]])
9. \-methods::cacheMetaData(ns, TRUE, ns)
   10.   \-methods:::.doLoadActions(where, attach)

  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ... [5s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(scDiffCom)
  >
  > test_check("scDiffCom")
  Loading required package: SeuratObject

---

Since I have no error locally on my machine, I don't know what I could
change for the automatic tests to work. Also, I don't understand why
the github-action for windows-latest (release) works but not
devtools:check_win_release().

By the way, I installed R devel on my machine in addition to R 4.1.0,
but it turns out I cannot test our package installation because it has
Bioconductor dependencies and "Bioconductor does not yet build and
check packages for R version 4.2" as reported here
. The exact same error
actually also occurs when I run devtools:check_rhub(). It does not
seem to be related to the failure of testthat I reported above, but I
thought it might be useful to mention it.

Thanks in advance for any help/suggestions!

Cyril

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] ERROR: lazy loading failed for package 'movecost'

2021-07-04 Thread Gianmarco Alberti

Hello,

I am in the process of checking my ‘movecost’ package before submitting to CRAN.

As usual, I have tested my package locally (on my MAC) using devtools::check() 
and everything is fine, getting 0 error, 0 warnings and 0 notes.

Also, as I routinely do, I used (A) devtools::check_win_devel(); in the 
returned email, the status was OK 
(https://win-builder.r-project.org/lWar6m662wl3).

BUT, I got 1 error from both:
(B) devtools::check_win_release() 
(https://win-builder.r-project.org/6ZzaipUr9rPF)
(C) devtools::check_win_oldrelease() 
(https://win-builder.r-project.org/yXHZoOCov7xH)

I cannot really figure out what is actually causing the error (Im not a 
specialist in programming and the like):
ERROR: lazy loading failed for package ‘movecost'


Any hint/elucidation on the matter, so that I can spot what is causing the 
error, would be appreciated.
Thank you for your time and consideration.

Best
Gianmarco



Dr Gianmarco Alberti (PhD Udine)
Lecturer in Spatial Forensics
Coordinator of the BA dissertations
Department of Criminology
Faculty for Social Wellbeing
Room 332, Humanities B (FEMA)
University of Malta, Msida, Malta (Europe) - MSD 2080
tel +356 2340 3718

Academic profiles
https://www.researchgate.net/profile/Gianmarco_Alberti4
https://malta.academia.edu/GianmarcoAlberti

Google Scholar profile
https://scholar.google.com/citations?user=tFrJKQ0J=en

Correspondence Analysis website
http://cainarchaeology.weebly.com/

R packages on CRAN:
CAinterprTools
https://cran.r-project.org/web/packages/CAinterprTools/index.html

GmAMisc
https://cran.r-project.org/package=GmAMisc

movecost
https://cran.r-project.org/web/packages/movecost/index.html


[[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] R-CMD-check works locally and on github, but windows automatic checks fail

[R-pkg-devel] R-CMD-check works locally and on github, but windows automatic checks fail

[R-pkg-devel] ERROR: lazy loading failed for package 'movecost'

3 matches

Site Navigation

Mail list logo

Footer information