* using log directory 'd:/Rcompile/CRANpkg/local/3.5/libcoin.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'libcoin/DESCRIPTION' ... OK
* this is package 'libcoin' version '1.0-5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'libcoin' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Problems with news in 'inst/NEWS.Rd':
  inst/NEWS.Rd:10: unknown macro '\proglang'
  inst/NEWS.Rd:47: unknown macro '\proglang'
  inst/NEWS.Rd:69: unknown macro '\proglang'
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [1s] OK
** checking differences from 'libcoin-Ex_i386.Rout' to 'libcoin-Ex.Rout.save' ... OK
** running examples for arch 'x64' ... [1s] OK
** checking differences from 'libcoin-Ex_x64.Rout' to 'libcoin-Ex.Rout.save' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ... [18s] OK
  Running 'bugfixes.R' [1s]
  Comparing 'bugfixes.Rout' to 'bugfixes.Rout.save' ... OK
  Running 'regtest_ctabs.R' [1s]
  Comparing 'regtest_ctabs.Rout' to 'regtest_ctabs.Rout.save' ... OK
  Running 'regtest_libcoin.R' [16s]
  Comparing 'regtest_libcoin.Rout' to 'regtest_libcoin.Rout.save' ...377c377
< maxT = 1.6358, p-value = 0.61
---
> maxT = 2.1537, p-value = 0.26
380c380
<   "best" cutpoint: <= 0.82
---
>   "best" cutpoint: <= 0.53
385c385
< [1] 1.635842
---
> [1] 2.153664
388c388
< [1] 0.596
---
> [1] 0.245
391c391
< [1] 56
---
> [1] 36
395c395
< [1] 0.82
---
> [1] 0.53
398c398
< [1] 2.67598
---
> [1] 4.63827
401c401
< [1] 0.596
---
> [1] 0.245
404c404
< [1] 56
---
> [1] 36
408c408
< [1] 0.82
---
> [1] 0.53
412c412
< [1] 1.635842
---
> [1] 2.153664
415c415
< [1] 0.614
---
> [1] 0.253
418c418
< [1] 56
---
> [1] 36
422c422
< [1] 0.82
---
> [1] 0.53
425c425
< [1] 2.67598
---
> [1] 4.63827
428c428
< [1] 0.614
---
> [1] 0.253
431c431
< [1] 56
---
> [1] 36
435c435
< [1] 0.82
---
> [1] 0.53
443c443
< maxT = 1.6169, p-value = 0.627
---
> maxT = 2.2764, p-value = 0.221
446c446
<   "best" cutpoint: <= 0.38
---
>   "best" cutpoint: <= 0.53
451c451
< [1] 1.616943
---
> [1] 2.276446
454c454
< [1] 0.603
---
> [1] 0.192
457c457
< [1] 26
---
> [1] 36
461c461
< [1] 0.38
---
> [1] 0.53
464c464
< [1] 2.614503
---
> [1] 5.182204
467c467
< [1] 0.603
---
> [1] 0.192
470c470
< [1] 26
---
> [1] 36
474c474
< [1] 0.38
---
> [1] 0.53
485c485
< maxT = 1.8369, p-value = 0.695
---
> maxT = 2.1537, p-value = 0.445
488c488
<   "best" cutpoint: <= 0.26
---
>   "best" cutpoint: <= 0.53
493c493
< [1] 1.836908
---
> [1] 2.153664
496c496
< [1] 0.724
---
> [1] 0.471
499c499
< [1] 18
---
> [1] 36
503c503
< [1] 0.26
---
> [1] 0.53
506c506
< [1] 3.978233
---
> [1] 5.720153
509c509
< [1] 0.73
---
> [1] 0.412
512c512
< [1] 42
---
> [1] 40
515c515
< [1] 0.6
---
> [1] 0.57
519c519
< [1] 1.836908
---
> [1] 2.153664
522c522
< [1] 0.683
---
> [1] 0.476
525c525
< [1] 18
---
> [1] 36
529c529
< [1] 0.26
---
> [1] 0.53
532c532
< [1] 3.978233
---
> [1] 5.720153
535c535
< [1] 0.685
---
> [1] 0.429
538c538
< [1] 42
---
> [1] 40
541c541
< [1] 0.6
---
> [1] 0.57
549c549
< maxT = 1.6169, p-value = 0.843
---
> maxT = 2.2764, p-value = 0.38
552c552
<   "best" cutpoint: <= 0.38
---
>   "best" cutpoint: <= 0.53
557c557
< [1] 1.616943
---
> [1] 2.276446
560c560
< [1] 0.844
---
> [1] 0.394
563c563
< [1] 26
---
> [1] 36
567c567
< [1] 0.38
---
> [1] 0.53
570c570
< [1] 3.122189
---
> [1] 5.406605
573c573
< [1] 0.843
---
> [1] 0.504
576c576
< [1] 26
---
> [1] 40
579c579
< [1] 0.38
---
> [1] 0.57
596c596
< maxT = 2.6462, p-value = 0.077
---
> maxT = 1.7088, p-value = 0.443
599c599
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3} vs. {2, 4, 5}
604c604
< [1] 2.646215
---
> [1] 1.708775
607c607
< [1] 0.065
---
> [1] 0.485
610c610
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
615c615
< [1] 7.002453
---
> [1] 2.919912
618c618
< [1] 0.065
---
> [1] 0.485
621c621
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
627c627
< [1] 2.646215
---
> [1] 1.708775
630c630
< [1] 0.066
---
> [1] 0.476
633c633
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
638c638
< [1] 7.002453
---
> [1] 2.919912
641c641
< [1] 0.066
---
> [1] 0.476
644c644
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
654c654
< maxT = 2.6113, p-value = 0.084
---
> maxT = 1.6489, p-value = 0.543
657c657
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3} vs. {2, 4, 5}
662c662
< [1] 2.611339
---
> [1] 1.648947
665c665
< [1] 0.082
---
> [1] 0.464
668c668
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
673c673
< [1] 6.819091
---
> [1] 2.719028
676c676
< [1] 0.082
---
> [1] 0.464
679c679
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
692c692
< maxT = 2.6462, p-value = 0.126
---
> maxT = 2.358, p-value = 0.285
695c695
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3, 5} vs. {2, 4}
700c700
< [1] 2.646215
---
> [1] 2.357973
703c703
< [1] 0.146
---
> [1] 0.301
706c706
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
711c711
< [1] 7.94209
---
> [1] 8.373114
714c714
< [1] 0.181
---
> [1] 0.143
717c717
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
722c722
< [1] 2.646215
---
> [1] 2.357973
725c725
< [1] 0.145
---
> [1] 0.275
728c728
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
733c733
< [1] 7.94209
---
> [1] 8.373114
736c736
< [1] 0.172
---
> [1] 0.134
739c739
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
748c748
< maxT = 2.6113, p-value = 0.164
---
> maxT = 2.4473, p-value = 0.218
751c751
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3, 5} vs. {2, 4}
756c756
< [1] 2.611339
---
> [1] 2.447272
759c759
< [1] 0.16
---
> [1] 0.2
762c762
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
767c767
< [1] 7.823381
---
> [1] 8.115438
770c770
< [1] 0.18
---
> [1] 0.12
773c773
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
783c783
< chi-squared = 7.8234, df = 2, p-value = 0.02001
---
> chi-squared = 8.1154, df = 2, p-value = 0.01729
** running tests for arch 'x64' ... [18s] OK
  Running 'bugfixes.R' [1s]
  Comparing 'bugfixes.Rout' to 'bugfixes.Rout.save' ... OK
  Running 'regtest_ctabs.R' [1s]
  Comparing 'regtest_ctabs.Rout' to 'regtest_ctabs.Rout.save' ... OK
  Running 'regtest_libcoin.R' [16s]
  Comparing 'regtest_libcoin.Rout' to 'regtest_libcoin.Rout.save' ...377c377
< maxT = 1.6358, p-value = 0.61
---
> maxT = 2.1537, p-value = 0.26
380c380
<   "best" cutpoint: <= 0.82
---
>   "best" cutpoint: <= 0.53
385c385
< [1] 1.635842
---
> [1] 2.153664
388c388
< [1] 0.596
---
> [1] 0.245
391c391
< [1] 56
---
> [1] 36
395c395
< [1] 0.82
---
> [1] 0.53
398c398
< [1] 2.67598
---
> [1] 4.63827
401c401
< [1] 0.596
---
> [1] 0.245
404c404
< [1] 56
---
> [1] 36
408c408
< [1] 0.82
---
> [1] 0.53
412c412
< [1] 1.635842
---
> [1] 2.153664
415c415
< [1] 0.614
---
> [1] 0.253
418c418
< [1] 56
---
> [1] 36
422c422
< [1] 0.82
---
> [1] 0.53
425c425
< [1] 2.67598
---
> [1] 4.63827
428c428
< [1] 0.614
---
> [1] 0.253
431c431
< [1] 56
---
> [1] 36
435c435
< [1] 0.82
---
> [1] 0.53
443c443
< maxT = 1.6169, p-value = 0.627
---
> maxT = 2.2764, p-value = 0.221
446c446
<   "best" cutpoint: <= 0.38
---
>   "best" cutpoint: <= 0.53
451c451
< [1] 1.616943
---
> [1] 2.276446
454c454
< [1] 0.603
---
> [1] 0.192
457c457
< [1] 26
---
> [1] 36
461c461
< [1] 0.38
---
> [1] 0.53
464c464
< [1] 2.614503
---
> [1] 5.182204
467c467
< [1] 0.603
---
> [1] 0.192
470c470
< [1] 26
---
> [1] 36
474c474
< [1] 0.38
---
> [1] 0.53
485c485
< maxT = 1.8369, p-value = 0.695
---
> maxT = 2.1537, p-value = 0.445
488c488
<   "best" cutpoint: <= 0.26
---
>   "best" cutpoint: <= 0.53
493c493
< [1] 1.836908
---
> [1] 2.153664
496c496
< [1] 0.724
---
> [1] 0.471
499c499
< [1] 18
---
> [1] 36
503c503
< [1] 0.26
---
> [1] 0.53
506c506
< [1] 3.978233
---
> [1] 5.720153
509c509
< [1] 0.73
---
> [1] 0.412
512c512
< [1] 42
---
> [1] 40
515c515
< [1] 0.6
---
> [1] 0.57
519c519
< [1] 1.836908
---
> [1] 2.153664
522c522
< [1] 0.683
---
> [1] 0.476
525c525
< [1] 18
---
> [1] 36
529c529
< [1] 0.26
---
> [1] 0.53
532c532
< [1] 3.978233
---
> [1] 5.720153
535c535
< [1] 0.685
---
> [1] 0.429
538c538
< [1] 42
---
> [1] 40
541c541
< [1] 0.6
---
> [1] 0.57
549c549
< maxT = 1.6169, p-value = 0.843
---
> maxT = 2.2764, p-value = 0.38
552c552
<   "best" cutpoint: <= 0.38
---
>   "best" cutpoint: <= 0.53
557c557
< [1] 1.616943
---
> [1] 2.276446
560c560
< [1] 0.844
---
> [1] 0.394
563c563
< [1] 26
---
> [1] 36
567c567
< [1] 0.38
---
> [1] 0.53
570c570
< [1] 3.122189
---
> [1] 5.406605
573c573
< [1] 0.843
---
> [1] 0.504
576c576
< [1] 26
---
> [1] 40
579c579
< [1] 0.38
---
> [1] 0.57
596c596
< maxT = 2.6462, p-value = 0.077
---
> maxT = 1.7088, p-value = 0.443
599c599
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3} vs. {2, 4, 5}
604c604
< [1] 2.646215
---
> [1] 1.708775
607c607
< [1] 0.065
---
> [1] 0.485
610c610
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
615c615
< [1] 7.002453
---
> [1] 2.919912
618c618
< [1] 0.065
---
> [1] 0.485
621c621
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
627c627
< [1] 2.646215
---
> [1] 1.708775
630c630
< [1] 0.066
---
> [1] 0.476
633c633
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
638c638
< [1] 7.002453
---
> [1] 2.919912
641c641
< [1] 0.066
---
> [1] 0.476
644c644
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
654c654
< maxT = 2.6113, p-value = 0.084
---
> maxT = 1.6489, p-value = 0.543
657c657
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3} vs. {2, 4, 5}
662c662
< [1] 2.611339
---
> [1] 1.648947
665c665
< [1] 0.082
---
> [1] 0.464
668c668
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
673c673
< [1] 6.819091
---
> [1] 2.719028
676c676
< [1] 0.082
---
> [1] 0.464
679c679
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
692c692
< maxT = 2.6462, p-value = 0.126
---
> maxT = 2.358, p-value = 0.285
695c695
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3, 5} vs. {2, 4}
700c700
< [1] 2.646215
---
> [1] 2.357973
703c703
< [1] 0.146
---
> [1] 0.301
706c706
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
711c711
< [1] 7.94209
---
> [1] 8.373114
714c714
< [1] 0.181
---
> [1] 0.143
717c717
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
722c722
< [1] 2.646215
---
> [1] 2.357973
725c725
< [1] 0.145
---
> [1] 0.275
728c728
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
733c733
< [1] 7.94209
---
> [1] 8.373114
736c736
< [1] 0.172
---
> [1] 0.134
739c739
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 1
748c748
< maxT = 2.6113, p-value = 0.164
---
> maxT = 2.4473, p-value = 0.218
751c751
<   "best" cutpoint: {1, 3, 4, 5} vs. {2}
---
>   "best" cutpoint: {1, 3, 5} vs. {2, 4}
756c756
< [1] 2.611339
---
> [1] 2.447272
759c759
< [1] 0.16
---
> [1] 0.2
762c762
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
767c767
< [1] 7.823381
---
> [1] 8.115438
770c770
< [1] 0.18
---
> [1] 0.12
773c773
< [1] 0 1 0 0 0
---
> [1] 0 1 0 1 0
783c783
< chi-squared = 7.8234, df = 2, p-value = 0.02001
---
> chi-squared = 8.1154, df = 2, p-value = 0.01729
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... [3s] OK
* checking re-building of vignette outputs ... [31s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING