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bschneidr / svrep

Tools for Creating, Updating, and Analyzing Survey Replicate Weights
https://bschneidr.github.io/svrep/
GNU General Public License v3.0
7 stars 1 forks source link

Fix CRAN check issues by 9/15 #29

Closed bschneidr closed 1 year ago

bschneidr commented 1 year ago

From Brian Ripley:

Dear maintainer,

Please see the problems shown on https://cran.r-project.org/web/checks/check_results_svrep.html.

Please correct before 2023-09-15 to safely retain your package on CRAN.

Do remember to look at the 'Additional issues'.

The CRAN Team

https://cran.r-project.org/web/checks/check_results_svrep.html

A couple unit tests fail on the Atlas and MKL builds (interestingly, different ones fail).

Atlas Output ``` * using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/svrep.Rcheck’ * using R Under development (unstable) (2023-08-31 r85032) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘svrep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘svrep’ version ‘0.6.1’ * package encoding: UTF-8 * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘svrep’ can be installed ... [18s/48s] 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 ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [3s/11s] 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 ... [28s/61s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 12 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [7s/14s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [91s/162s] [91s/163s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(svrep) > > test_check("svrep") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 212 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-fays-generalized-replication.R:131:5'): Ultimate Cluster: Same results from conversion vs. creating from scratch ── `conversion_result` (`actual`) not equal to `orig_result` (`expected`). actual vs expected [, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [, 10] [, 11] [, 12] [, 13] [, 14] [, 15] [, 16] [, 17] [, 18] [, 19] [, 20] [, 21] [, 22] [, 23] [, 24] [, 25] [, 26] [, 27] [, 28] [, 29] [, 30] [, 31] [, 32] [, 33] [, 34] [, 35] [, 36] [, 37] [, 38] [, 39] [, 40] [, 41] [, 42] [, 43] [, 44] [, 45] [, 46] [, 47] [, 48] [, 49] [, 50] [, 51] [, 52] [, 53] [, 54] [, 55] [, 56] [, 57] [, 58] [, 59] [, 60] [, 61] [, 62] [, 63] [, 64] [, 65] [, 66] [, 67] [, 68] [, 69] [, 70] [, 71] [, 72] [, 73] [, 74] [, 75] [, 76] [, 77] [, 78] [, 79] [, 80] [, 81] [, 82] [, 83] [, 84] [, 85] [, 86] [, 87] [, 88] [, 89] [, 90] [, 91] [, 92] [, 93] [, 94] [, 95] [, 96] [, 97] [, 98] [, 99] [,100] [,101] [,102] [,103] [,104] - actual[1, ] 0.9360063 1.0196538 0.9109626 0.9660818 0.9219789 0.9498714 1.1211992 0.9779155 1.0466186 1.1679457 1.0302962 0.9109478 1.0485932 0.9272341 0.8527616 0.9495390 1.0807008 1.0097428 1.0738716 1.0361191 1.0252182 0.9910236 1.0098840 0.8319538 1.0027527 0.9327364 0.9660882 0.9961577 1.1493790 0.8269565 1.0567032 1.1317857 0.9602213 0.8484753 0.8650796 0.8442067 1.0602776 0.9433986 1.1421052 0.9639068 1.0387214 1.1605108 1.0096279 0.8791117 0.9560282 0.8889988 1.0331729 0.9056598 0.9985571 0.8935973 0.9733611 1.1197797 0.9148591 0.8953258 0.9943770 0.9491573 0.9923080 1.0677721 1.0256036 1.0765317 1.0954997 1.0049196 1.0624760 1.0586614 0.8786885 1.2099788 1.0507352 1.0769150 1.0918756 0.9695054 0.8263689 0.8933349 0.8855218 0.8372843 0.8807552 1.1269055 1.0419344 0.9762589 0.9816383 0.9234353 1.1380755 0.9043813 0.9602131 1.0369290 0.8709231 0.8868103 1.1376400 1.1909425 1.1481848 0.8968993 1.1263796 1.0847126 0.9642254 0.9954672 1.1493393 1.1134852 0.9818388 1.0860591 0.9273839 1.0402517 1.0761021 1.0610633 1.0800369 1.0146230 + expected[1, ] 1.1663899 1.0081160 1.0374951 0.9488619 0.9416496 1.1090158 1.1111921 0.9793891 0.9721103 1.1583285 0.8843017 0.9867592 1.1396005 1.0946185 0.8198171 0.8362498 1.0152756 1.0064335 1.1397815 0.9595651 1.0512068 0.8934859 1.0470493 0.9986920 1.1143437 0.9099915 1.0464555 0.9640762 0.9173713 0.8059782 0.8573696 0.9764359 0.9829940 0.9414453 1.0111687 0.8972151 1.0396309 0.9543246 1.0077093 0.9076267 1.1606708 0.9578686 1.0030971 0.8885520 0.8551721 1.0448448 0.9167982 0.9051984 0.8803515 1.1263698 1.1604919 1.1211849 1.0438201 0.9964538 0.8948716 0.9711699 0.8717214 0.8142525 1.0283202 0.9742947 1.1073033 0.8625816 1.1929894 1.1877359 0.9550405 0.9170065 1.1072480 1.1379947 0.9663909 1.0382219 0.8694436 0.9323811 0.9832288 1.0777911 1.0054338 0.8910870 0.9726759 1.0239061 1.1337864 1.1451838 1.0474215 1.0161920 0.9750929 0.9332798 1.0110818 1.0306353 1.0184548 1.0638946 0.9372287 1.1927475 1.0865799 1.0222167 1.1108732 0.9677275 0.8443316 1.0615862 0.9838113 1.0785368 1.0430755 0.9913680 0.9796819 0.9599188 0.9268569 0.9946769 - actual[2, ] 0.9360063 1.0196538 0.9109626 0.9660818 0.9219789 0.9498714 1.1211992 0.9779155 1.0466186 1.1679457 1.0302962 0.9109478 1.0485932 0.9272341 0.8527616 0.9495390 1.0807008 1.0097428 1.0738716 1.0361191 1.0252182 0.9910236 1.0098840 0.8319538 1.0027527 0.9327364 0.9660882 0.9961577 1.1493790 0.8269565 1.0567032 1.1317857 0.9602213 0.8484753 0.8650796 0.8442067 1.0602776 0.9433986 1.1421052 0.9639068 1.0387214 1.1605108 1.0096279 0.8791117 0.9560282 0.8889988 1.0331729 0.9056598 0.9985571 0.8935973 0.9733611 1.1197797 0.9148591 0.8953258 0.9943770 0.9491573 0.9923080 1.0677721 1.0256036 1.0765317 1.0954997 1.0049196 1.0624760 1.0586614 0.8786885 1.2099788 1.0507352 1.0769150 1.0918756 0.9695054 0.8263689 0.8933349 0.8855218 0.8372843 0.8807552 1.1269055 1.0419344 0.9762589 0.9816383 0.9234353 1.1380755 0.9043813 0.9602131 1.0369290 0.8709231 0.8868103 1.1376400 1.1909425 1.1481848 0.8968993 1.1263796 1.0847126 0.9642254 0.9954672 1.1493393 1.1134852 0.9818388 1.0860591 0.9273839 1.0402517 1.0761021 1.0610633 1.0800369 1.0146230 + expected[2, ] 1.1663899 1.0081160 1.0374951 0.9488619 0.9416496 1.1090158 1.1111921 0.9793891 0.9721103 1.1583285 0.8843017 0.9867592 1.1396005 1.0946185 0.8198171 0.8362498 1.0152756 1.0064335 1.1397815 0.9595651 1.0512068 0.8934859 1.0470493 0.9986920 1.1143437 0.9099915 1.0464555 0.9640762 0.9173713 0.8059782 0.8573696 0.9764359 0.9829940 0.9414453 1.0111687 0.8972151 1.0396309 0.9543246 1.0077093 0.9076267 1.1606708 0.9578686 1.0030971 0.8885520 0.8551721 1.0448448 0.9167982 0.9051984 0.8803515 1.1263698 1.1604919 1.1211849 1.0438201 0.9964538 0.8948716 0.9711699 0.8717214 0.8142525 1.0283202 0.9742947 1.1073033 0.8625816 1.1929894 1.1877359 0.9550405 0.9170065 1.1072480 1.1379947 0.9663909 1.0382219 0.8694436 0.9323811 0.9832288 1.0777911 1.0054338 0.8910870 0.9726759 1.0239061 1.1337864 1.1451838 1.0474215 1.0161920 0.9750929 0.9332798 1.0110818 1.0306353 1.0184548 1.0638946 0.9372287 1.1927475 1.0865799 1.0222167 1.1108732 0.9677275 0.8443316 1.0615862 0.9838113 1.0785368 1.0430755 0.9913680 0.9796819 0.9599188 0.9268569 0.9946769 - actual[3, ] 1.0602865 0.9139103 0.8664832 1.1056325 0.9402090 0.9126872 1.0589346 1.1229858 1.0503414 0.8711682 0.9543921 0.9288411 1.0061486 1.0651445 0.9566318 0.9584447 1.0264615 1.0056752 1.1487917 0.9431762 0.9507878 0.8608131 1.2255785 1.0525044 1.0027525 0.9010933 1.1353207 0.9537982 1.1159785 1.0473159 0.8072744 0.9739615 0.9952893 0.8248166 1.1256655 1.0706404 0.9511751 0.9334424 0.8926206 1.1166457 1.1136345 1.0560099 0.9840984 1.0476762 0.9957995 1.1274066 1.0154424 0.9569388 1.0291789 0.9803537 0.9264530 1.0558765 0.9990444 1.0673520 0.9164760 1.0450805 0.8977918 1.0375730 1.1307560 0.9550018 0.9218387 0.9705367 1.0725629 0.9785977 0.7932964 1.1029818 0.8119809 0.9071886 0.9740264 0.9474872 1.0436593 0.9834512 1.0828878 0.9451257 0.9174677 0.9126856 1.0522187 1.1809385 0.8244872 1.1260533 0.9670161 1.1715893 1.0987859 1.1370989 0.9988806 0.9885606 1.0485753 1.0513006 0.8798970 0.9205836 1.0448834 1.1033679 1.1406205 1.0313341 0.9612673 1.0278465 0.9542976 1.1356294 1.0701513 1.1318938 1.0670915 0.8890539 0.8126041 1.0074916 + expected[3, ] 0.9579247 1.0001589 0.9900231 0.9572585 0.9364528 0.9154137 1.0481280 1.1325650 1.0937197 1.1124461 1.0449125 0.8367526 0.8331574 0.8893437 0.9696384 1.1202919 1.1592380 0.9480145 1.1383162 0.8990895 1.1295205 0.9937041 0.8963971 0.9854375 0.9161422 0.9635610 0.9691933 0.9573218 0.9726756 0.9400018 0.8768299 0.9374394 1.0286658 0.8696392 1.0488076 0.8894465 0.9747076 0.9070810 0.9923403 1.1445268 0.9208185 1.0378473 0.8247891 1.0750547 1.1930925 0.9669520 1.0884151 0.9187419 1.1142107 1.1575763 0.9407297 0.9827064 0.9830347 1.0463730 1.0226791 1.0564239 0.8995310 0.7845494 1.0693977 0.9961007 1.0602593 1.0970715 1.0015452 1.1404034 0.9882157 1.0754614 1.0541487 0.9538596 1.1052488 1.0036126 0.9647929 1.0078285 1.0020315 1.0514558 1.0712584 1.0056999 1.0709262 1.1055076 0.9464850 0.9128288 1.1661713 1.1904391 0.9267572 1.1306879 0.9591649 0.9098599 0.8954301 0.9762428 0.8810802 0.9877874 0.9151790 0.9826795 1.0069804 1.1037292 1.1948379 0.9863978 1.0686932 1.1654956 0.9139607 1.1659858 0.8608982 1.0035835 0.8679435 0.9883893 - actual[4, ] 1.0602865 0.9139103 0.8664832 1.1056325 0.9402090 0.9126872 1.0589346 1.1229858 1.0503414 0.8711682 0.9543921 0.9288411 1.0061486 1.0651445 0.9566318 0.9584447 1.0264615 1.0056752 1.1487917 0.9431762 0.9507878 0.8608131 1.2255785 1.0525044 1.0027525 0.9010933 1.1353207 0.9537982 1.1159785 1.0473159 0.8072744 0.9739615 0.9952893 0.8248166 1.1256655 1.0706404 0.9511751 0.9334424 0.8926206 1.1166457 1.1136345 1.0560099 0.9840984 1.0476762 0.9957995 1.1274066 1.0154424 0.9569388 1.0291789 0.9803537 0.9264530 1.0558765 0.9990444 1.0673520 0.9164760 1.0450805 0.8977918 1.0375730 1.1307560 0.9550018 0.9218387 0.9705367 1.0725629 0.9785977 0.7932964 1.1029818 0.8119809 0.9071886 0.9740264 0.9474872 1.0436593 0.9834512 1.0828878 0.9451257 0.9174677 0.9126856 1.0522187 1.1809385 0.8244872 1.1260533 0.9670161 1.1715893 1.0987859 1.1370989 0.9988806 0.9885606 1.0485753 1.0513006 0.8798970 0.9205836 1.0448834 1.1033679 1.1406205 1.0313341 0.9612673 1.0278465 0.9542976 1.1356294 1.0701513 1.1318938 1.0670915 0.8890539 0.8126041 1.0074916 + expected[4, ] 0.9579247 1.0001589 0.9900231 0.9572585 0.9364528 0.9154137 1.0481280 1.1325650 1.0937197 1.1124461 1.0449125 0.8367526 0.8331574 0.8893437 0.9696384 1.1202919 1.1592380 0.9480145 1.1383162 0.8990895 1.1295205 0.9937041 0.8963971 0.9854375 0.9161422 0.9635610 0.9691933 0.9573218 0.9726756 0.9400018 0.8768299 0.9374394 1.0286658 0.8696392 1.0488076 0.8894465 0.9747076 0.9070810 0.9923403 1.1445268 0.9208185 1.0378473 0.8247891 1.0750547 1.1930925 0.9669520 1.0884151 0.9187419 1.1142107 1.1575763 0.9407297 0.9827064 0.9830347 1.0463730 1.0226791 1.0564239 0.8995310 0.7845494 1.0693977 0.9961007 1.0602593 1.0970715 1.0015452 1.1404034 0.9882157 1.0754614 1.0541487 0.9538596 1.1052488 1.0036126 0.9647929 1.0078285 1.0020315 1.0514558 1.0712584 1.0056999 1.0709262 1.1055076 0.9464850 0.9128288 1.1661713 1.1904391 0.9267572 1.1306879 0.9591649 0.9098599 0.8954301 0.9762428 0.8810802 0.9877874 0.9151790 0.9826795 1.0069804 1.1037292 1.1948379 0.9863978 1.0686932 1.1654956 0.9139607 1.1659858 0.8608982 1.0035835 0.8679435 0.9883893 - actual[5, ] 1.0601345 0.9910464 1.0514350 1.0033002 1.1236701 1.0290118 0.9692789 1.0496231 0.8714809 1.0819658 1.0261872 1.0900422 1.2460501 0.9183494 0.9985243 1.2506044 0.9754757 1.0446088 0.8366895 0.8962881 1.0635593 0.9585632 1.1261877 0.9098370 0.9243423 1.0219386 1.0105398 0.9629104 0.8860892 0.9640589 1.0767151 1.0050734 0.8109712 0.9379737 1.1009605 1.0852743 1.0204562 0.9194938 0.9425757 0.9320227 1.0790743 1.0176857 0.8465016 0.9412995 0.9187206 0.9809585 1.0426621 0.8363106 0.9871942 1.0571283 1.1064098 0.8687611 1.1023279 1.0805700 1.0094792 1.1165428 1.1379099 1.0311803 1.1136413 1.0312609 1.0469585 0.8104032 0.9676728 0.9675381 0.9998214 1.0517194 0.9035224 0.8274084 0.9574743 0.9929685 0.9861204 1.0156252 1.0415482 1.0343993 1.0881064 1.1193279 1.0828301 1.0289519 0.9540219 0.9409525 1.1794978 1.0426346 0.9305911 1.0169429 0.9883099 0.7421340 0.8223238 1.0875234 1.0167912 1.0103949 0.9728107 0.8867724 1.0282343 0.9663772 0.9562490 1.2010413 1.0943035 1.0234460 0.9181740 0.9190719 0.9072129 0.9566647 0.9445349 1.1278404 + expected[5, ] 1.1227104 0.8376214 0.9694528 1.0782400 1.1255299 1.1148107 0.9920549 0.9757858 0.9136419 1.0729945 1.1755977 1.0614954 1.0585635 0.8890117 0.9630950 0.8889109 1.0034056 1.0484854 0.9589370 0.8650603 0.9138272 0.9725810 1.0752946 0.9752421 0.9634789 1.1415234 1.2086539 0.9690167 1.0569502 1.0356424 1.0640438 1.0901008 0.9383474 0.9933340 1.0221982 1.1381185 0.9854594 0.9259058 1.0120091 0.9120466 1.1025779 1.0636902 0.8765623 1.0785289 0.9641806 1.0440629 1.0104961 0.8410669 1.1128087 0.9826449 1.1097905 0.9395196 1.2069601 0.7883971 0.8345490 1.1361562 0.9248951 0.9583726 1.0846876 0.9772203 1.0547887 1.0081401 1.0209291 1.0242880 0.9555206 1.0081852 0.9355902 0.8382858 0.9077076 0.9164895 0.9222649 0.9869591 1.1938348 1.0054182 0.9198786 1.1467068 0.9899782 0.8560354 0.8285861 0.9453541 0.9765364 1.0517502 0.9645646 0.9919964 1.0252828 0.8912027 0.8668757 0.9986785 0.9187940 0.9609526 1.1425114 0.8836236 0.8202312 1.1682477 0.9954438 0.9778654 0.9868565 1.1186164 1.0260937 1.0262931 1.0823453 1.0605250 1.0711549 1.0498794 - actual[6, ] 1.0601345 0.9910464 1.0514350 1.0033002 1.1236701 1.0290118 0.9692789 1.0496231 0.8714809 1.0819658 1.0261872 1.0900422 1.2460501 0.9183494 0.9985243 1.2506044 0.9754757 1.0446088 0.8366895 0.8962881 1.0635593 0.9585632 1.1261877 0.9098370 0.9243423 1.0219386 1.0105398 0.9629104 0.8860892 0.9640589 1.0767151 1.0050734 0.8109712 0.9379737 1.1009605 1.0852743 1.0204562 0.9194938 0.9425757 0.9320227 1.0790743 1.0176857 0.8465016 0.9412995 0.9187206 0.9809585 1.0426621 0.8363106 0.9871942 1.0571283 1.1064098 0.8687611 1.1023279 1.0805700 1.0094792 1.1165428 1.1379099 1.0311803 1.1136413 1.0312609 1.0469585 0.8104032 0.9676728 0.9675381 0.9998214 1.0517194 0.9035224 0.8274084 0.9574743 0.9929685 0.9861204 1.0156252 1.0415482 1.0343993 1.0881064 1.1193279 1.0828301 1.0289519 0.9540219 0.9409525 1.1794978 1.0426346 0.9305911 1.0169429 0.9883099 0.7421340 0.8223238 1.0875234 1.0167912 1.0103949 0.9728107 0.8867724 1.0282343 0.9663772 0.9562490 1.2010413 1.0943035 1.0234460 0.9181740 0.9190719 0.9072129 0.9566647 0.9445349 1.1278404 + expected[6, ] 1.1227104 0.8376214 0.9694528 1.0782400 1.1255299 1.1148107 0.9920549 0.9757858 0.9136419 1.0729945 1.1755977 1.0614954 1.0585635 0.8890117 0.9630950 0.8889109 1.0034056 1.0484854 0.9589370 0.8650603 0.9138272 0.9725810 1.0752946 0.9752421 0.9634789 1.1415234 1.2086539 0.9690167 1.0569502 1.0356424 1.0640438 1.0901008 0.9383474 0.9933340 1.0221982 1.1381185 0.9854594 0.9259058 1.0120091 0.9120466 1.1025779 1.0636902 0.8765623 1.0785289 0.9641806 1.0440629 1.0104961 0.8410669 1.1128087 0.9826449 1.1097905 0.9395196 1.2069601 0.7883971 0.8345490 1.1361562 0.9248951 0.9583726 1.0846876 0.9772203 1.0547887 1.0081401 1.0209291 1.0242880 0.9555206 1.0081852 0.9355902 0.8382858 0.9077076 0.9164895 0.9222649 0.9869591 1.1938348 1.0054182 0.9198786 1.1467068 0.9899782 0.8560354 0.8285861 0.9453541 0.9765364 1.0517502 0.9645646 0.9919964 1.0252828 0.8912027 0.8668757 0.9986785 0.9187940 0.9609526 1.1425114 0.8836236 0.8202312 1.1682477 0.9954438 0.9778654 0.9868565 1.1186164 1.0260937 1.0262931 1.0823453 1.0605250 1.0711549 1.0498794 - actual[7, ] 0.8562064 1.1142957 1.0010809 0.9926135 1.0434795 1.0237077 0.9312796 0.9994839 1.0528643 0.9597210 1.0924735 1.0403818 0.9735086 0.9218487 1.1066424 0.9392748 1.1888139 0.8931059 1.0761796 1.1475808 1.0529432 1.0213832 1.0428660 0.9563207 0.8999591 1.0084781 1.0280009 0.8731874 1.0430478 0.9263495 0.8819238 0.8769902 0.9315143 0.9949732 1.1789490 0.8930293 1.0631025 1.0839207 1.1274882 0.9883121 0.9234804 0.8797367 1.1819586 0.9204771 0.8772673 0.9788258 1.1076216 1.2083795 0.8787048 1.1008375 0.9823947 0.9465381 1.0446582 0.9283610 0.9726202 1.1033262 0.9838459 0.8605491 0.9268632 1.1174824 1.0917729 0.9186722 1.2183401 1.1462619 0.9484548 1.1786174 1.0080840 0.8086211 1.1586718 0.8306687 0.9383496 1.0998928 0.9902050 1.1088919 1.0248450 1.0379128 0.8187079 0.9547180 0.9708297 1.0329320 1.0216554 0.9832572 1.0536596 0.9860384 1.1513816 0.9862834 0.9767542 0.8723473 1.0262385 1.0736965 0.9305191 1.0480639 0.9918433 0.9452160 0.8740010 1.0695732 1.0146802 1.0527021 0.9608921 1.0748839 0.9869707 1.0859633 0.9065959 1.0817933 + expected[7, ] 0.9982183 0.9973372 0.8719663 1.0302989 1.0461334 1.0163736 0.8653981 1.0236075 0.9526916 0.9215582 1.0819698 0.9708103 0.9089027 1.0814903 0.8308871 1.0334688 0.9671511 0.7764084 1.0400418 0.7593192 1.0357115 1.1022498 0.9951364 0.9057226 1.0617125 1.0193618 0.9889651 1.1577830 1.0422756 1.0164395 0.9813125 1.0409132 0.9105168 0.9864934 0.9053695 0.8905938 1.1237811 1.0805459 1.1120393 1.0827216 0.9749686 1.1429854 1.0334360 1.1301007 1.1002659 1.1036872 0.9314187 1.1868270 0.9028044 0.9859531 1.0681666 0.8700592 1.0620699 0.9704287 0.9626673 0.8445399 1.0549976 0.9250606 0.8948680 0.9009129 1.1260121 0.9224699 1.1368774 0.9948500 0.8641166 0.9793634 0.9042680 0.8725233 0.9471558 0.9293836 0.9229649 1.1653036 1.0185482 0.8764924 1.0013075 1.0938077 0.9358540 1.0313340 0.9374497 1.0323971 1.0234742 1.0320573 1.0883908 1.0086524 0.7899573 1.1318575 1.0860774 1.0731572 0.9952424 1.1724176 0.9600340 1.1314688 1.0280460 0.9036979 1.0678164 0.8743811 0.8642282 0.9507735 1.0763141 0.9943055 0.9637727 1.1414992 0.9717717 1.0708003 - actual[8, ] 0.8562064 1.1142957 1.0010809 0.9926135 1.0434795 1.0237077 0.9312796 0.9994839 1.0528643 0.9597210 1.0924735 1.0403818 0.9735086 0.9218487 1.1066424 0.9392748 1.1888139 0.8931059 1.0761796 1.1475808 1.0529432 1.0213832 1.0428660 0.9563207 0.8999591 1.0084781 1.0280009 0.8731874 1.0430478 0.9263495 0.8819238 0.8769902 0.9315143 0.9949732 1.1789490 0.8930293 1.0631025 1.0839207 1.1274882 0.9883121 0.9234804 0.8797367 1.1819586 0.9204771 0.8772673 0.9788258 1.1076216 1.2083795 0.8787048 1.1008375 0.9823947 0.9465381 1.0446582 0.9283610 0.9726202 1.1033262 0.9838459 0.8605491 0.9268632 1.1174824 1.0917729 0.9186722 1.2183401 1.1462619 0.9484548 1.1786174 1.0080840 0.8086211 1.1586718 0.8306687 0.9383496 1.0998928 0.9902050 1.1088919 1.0248450 1.0379128 0.8187079 0.9547180 0.9708297 1.0329320 1.0216554 0.9832572 1.0536596 0.9860384 1.1513816 0.9862834 0.9767542 0.8723473 1.0262385 1.0736965 0.9305191 1.0480639 0.9918433 0.9452160 0.8740010 1.0695732 1.0146802 1.0527021 0.9608921 1.0748839 0.9869707 1.0859633 0.9065959 1.0817933 + expected[8, ] 0.9982183 0.9973372 0.8719663 1.0302989 1.0461334 1.0163736 0.8653981 1.0236075 0.9526916 0.9215582 1.0819698 0.9708103 0.9089027 1.0814903 0.8308871 1.0334688 0.9671511 0.7764084 1.0400418 0.7593192 1.0357115 1.1022498 0.9951364 0.9057226 1.0617125 1.0193618 0.9889651 1.1577830 1.0422756 1.0164395 0.9813125 1.0409132 0.9105168 0.9864934 0.9053695 0.8905938 1.1237811 1.0805459 1.1120393 1.0827216 0.9749686 1.1429854 1.0334360 1.1301007 1.1002659 1.1036872 0.9314187 1.1868270 0.9028044 0.9859531 1.0681666 0.8700592 1.0620699 0.9704287 0.9626673 0.8445399 1.0549976 0.9250606 0.8948680 0.9009129 1.1260121 0.9224699 1.1368774 0.9948500 0.8641166 0.9793634 0.9042680 0.8725233 0.9471558 0.9293836 0.9229649 1.1653036 1.0185482 0.8764924 1.0013075 1.0938077 0.9358540 1.0313340 0.9374497 1.0323971 1.0234742 1.0320573 1.0883908 1.0086524 0.7899573 1.1318575 1.0860774 1.0731572 0.9952424 1.1724176 0.9600340 1.1314688 1.0280460 0.9036979 1.0678164 0.8743811 0.8642282 0.9507735 1.0763141 0.9943055 0.9637727 1.1414992 0.9717717 1.0708003 - actual[9, ] 0.9839574 0.9520997 0.9046410 1.1067446 1.0167071 0.9443550 0.8050576 0.9679825 1.1235686 1.0801993 0.9082235 1.1157319 0.8972025 0.9705706 1.0405728 0.8983991 1.0085045 1.0428309 1.0628084 0.7022068 1.1332512 0.9606836 1.0581170 1.1457279 1.1643097 1.0262352 0.9566223 0.9556768 1.0558008 0.8653595 1.0160211 0.8843179 1.0647020 1.0201130 0.9944452 0.9390252 0.8325935 1.0162026 0.9136889 1.1482364 1.0673632 0.9642506 1.0258746 0.9240219 0.9578667 0.9115805 1.0056656 0.9551393 1.0213113 1.0180766 0.9812224 1.1110290 1.0666304 1.1994187 1.1394899 0.9524258 1.0570481 1.0212788 1.1511561 0.8759356 1.0971663 1.0358933 1.0331858 1.0615156 0.9573259 0.9104191 0.9492882 1.0606599 1.1114558 1.1362587 0.8529438 1.0345002 0.9330035 0.9261810 0.9483923 0.9543204 0.8967357 1.0054756 0.9897818 1.0378075 0.9345840 0.8740067 0.9407307 1.0051000 1.1348545 0.9678975 0.9985084 1.0439207 1.2271451 1.0996814 0.8489468 0.8123722 0.9384849 0.9352699 0.8994582 1.0568010 1.0896017 1.1494721 1.0549154 1.0162329 0.8801098 0.9973694 1.0822742 0.9938509 + expected[9, ] 1.0834719 1.0248528 0.9814229 1.1451153 1.0522231 0.9820120 0.9502661 1.1152537 1.0575280 0.9231458 0.9998753 1.1648495 1.0338748 1.0352392 0.9837036 1.0074083 0.9803614 0.9761106 1.2274478 1.0279462 1.0924665 1.0845263 0.9875306 1.0394955 1.1064453 1.0913074 0.9467187 0.8310549 1.0236496 1.0963248 0.9067810 0.9539350 1.0626994 0.8770030 0.9625751 1.0270191 0.9056820 0.9854324 1.0030501 0.9289935 1.0109813 1.2371347 1.0157712 0.8974509 0.9544119 0.9008959 0.8928500 0.9861240 0.9745342 0.9633234 0.9930044 0.9946842 1.0481440 1.0866698 1.0953174 0.9687197 1.0539306 0.8870166 1.1408745 0.9400054 0.9364602 1.0838924 0.9996077 1.0503206 1.1176343 1.1699224 1.0988451 0.9327106 0.9293526 1.0748399 0.9788639 0.8800972 0.9759901 0.7896013 0.9352756 0.9588039 0.7363588 0.9273480 0.8720359 1.1732353 0.9271909 1.0931819 0.9913567 0.9531504 0.9494951 0.9512664 1.1813490 1.0020882 1.1516607 0.8991333 0.8538771 0.9960575 1.0556372 1.0985819 1.0427984 1.0338436 0.9949348 1.1565340 0.8908015 0.8617653 0.9554498 1.0085956 1.1841138 0.9680474 - actual[10, ] 0.9839574 0.9520997 0.9046410 1.1067446 1.0167071 0.9443550 0.8050576 0.9679825 1.1235686 1.0801993 0.9082235 1.1157319 0.8972025 0.9705706 1.0405728 0.8983991 1.0085045 1.0428309 1.0628084 0.7022068 1.1332512 0.9606836 1.0581170 1.1457279 1.1643097 1.0262352 0.9566223 0.9556768 1.0558008 0.8653595 1.0160211 0.8843179 1.0647020 1.0201130 0.9944452 0.9390252 0.8325935 1.0162026 0.9136889 1.1482364 1.0673632 0.9642506 1.0258746 0.9240219 0.9578667 0.9115805 1.0056656 0.9551393 1.0213113 1.0180766 0.9812224 1.1110290 1.0666304 1.1994187 1.1394899 0.9524258 1.0570481 1.0212788 1.1511561 0.8759356 1.0971663 1.0358933 1.0331858 1.0615156 0.9573259 0.9104191 0.9492882 1.0606599 1.1114558 1.1362587 0.8529438 1.0345002 0.9330035 0.9261810 0.9483923 0.9543204 0.8967357 1.0054756 0.9897818 1.0378075 0.9345840 0.8740067 0.9407307 1.0051000 1.1348545 0.9678975 0.9985084 1.0439207 1.2271451 1.0996814 0.8489468 0.8123722 0.9384849 0.9352699 0.8994582 1.0568010 1.0896017 1.1494721 1.0549154 1.0162329 0.8801098 0.9973694 1.0822742 0.9938509 + expected[10, ] 1.0834719 1.0248528 0.9814229 1.1451153 1.0522231 0.9820120 0.9502661 1.1152537 1.0575280 0.9231458 0.9998753 1.1648495 1.0338748 1.0352392 0.9837036 1.0074083 0.9803614 0.9761106 1.2274478 1.0279462 1.0924665 1.0845263 0.9875306 1.0394955 1.1064453 1.0913074 0.9467187 0.8310549 1.0236496 1.0963248 0.9067810 0.9539350 1.0626994 0.8770030 0.9625751 1.0270191 0.9056820 0.9854324 1.0030501 0.9289935 1.0109813 1.2371347 1.0157712 0.8974509 0.9544119 0.9008959 0.8928500 0.9861240 0.9745342 0.9633234 0.9930044 0.9946842 1.0481440 1.0866698 1.0953174 0.9687197 1.0539306 0.8870166 1.1408745 0.9400054 0.9364602 1.0838924 0.9996077 1.0503206 1.1176343 1.1699224 1.0988451 0.9327106 0.9293526 1.0748399 0.9788639 0.8800972 0.9759901 0.7896013 0.9352756 0.9588039 0.7363588 0.9273480 0.8720359 1.1732353 0.9271909 1.0931819 0.9913567 0.9531504 0.9494951 0.9512664 1.1813490 1.0020882 1.1516607 0.8991333 0.8538771 0.9960575 1.0556372 1.0985819 1.0427984 1.0338436 0.9949348 1.1565340 0.8908015 0.8617653 0.9554498 1.0085956 1.1841138 0.9680474 and 183 more ... [ FAIL 1 | WARN 0 | SKIP 0 | PASS 212 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [204s/270s] OK * checking PDF version of manual ... [13s/17s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-ATLAS/svrep.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 12:36.35, 420.36 + 23.48 ```
MKL Output ``` * using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/svrep.Rcheck’ * using R Under development (unstable) (2023-08-31 r85033) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘svrep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘svrep’ version ‘0.6.1’ * package encoding: UTF-8 * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘svrep’ can be installed ... [16s/21s] 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 ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * 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 ... [26s/32s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 12 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [70s/71s] [71s/71s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(svrep) > > test_check("svrep") [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-database-backed-designs.R:90:5'): Generalized replication works for database-backed designs ── db_result$repweights (`actual`) not equal to non_db_result$repweights (`expected`). actual vs expected [, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] - actual[1, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[1, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[2, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[2, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[3, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[3, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[4, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[4, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[5, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[5, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[6, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[6, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[7, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[7, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[8, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[8, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[9, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[9, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 - actual[10, ] 0.8364085 1.1635915 0.6905474 0.8364085 1.3094526 0.8364085 1.3094526 1.1635915 1.1635915 1.3094526 1.3094526 0.6905474 0.6905474 1.1635915 0.8364085 0.6905474 + expected[10, ] 0.6735743 1.3264257 0.8479513 1.2179673 1.1520487 1.3264257 0.7394929 1.2179673 0.7820327 0.8479513 1.2605071 1.1520487 0.7394929 0.6735743 0.7820327 1.2605071 and 173 more ... ── Failure ('test-database-backed-designs.R:92:5'): Generalized replication works for database-backed designs ── SE(svytotal(x = ~api00, db_result)) (`actual`) not equal to SE(svytotal(x = ~api00, non_db_result)) (`expected`). `actual`: 800997 `expected`: 886563 ── Failure ('test-fays-generalized-replication.R:167:5'): Multistage Stratified SRS: Same results from conversion vs. creating from scratch ── `conversion_result` (`actual`) not equal to `orig_result` (`expected`). actual vs expected [,1] [,2] [,3] [,4] [,5] - actual[1, ] 1.1105231 1.0519947 1.0768062 0.9517013 1.0114947 + expected[1, ] 0.9391174 1.1065729 1.0264972 1.1029140 1.0180054 - actual[2, ] 1.0789570 1.0843684 1.1085751 0.9838723 1.0439226 + expected[2, ] 0.9047809 1.0723886 1.0610724 1.0684909 1.0473857 - actual[3, ] 1.0105986 0.9445133 0.8832374 1.0611271 0.9644124 + expected[3, ] 0.9633092 1.0713948 0.9746474 1.0072710 0.9899692 - actual[4, ] 0.9633769 0.9844143 0.9231383 1.0212261 0.9245114 + expected[4, ] 1.0079378 1.1141765 1.0174291 0.9644893 0.9471875 - actual[5, ] 1.0425351 1.0381126 1.0680394 1.1401905 0.9626536 + expected[5, ] 1.0638396 0.9424794 1.0267196 0.8752555 1.0430815 - actual[6, ] 1.0871124 0.9939888 1.0239155 1.0956132 0.9180764 + expected[6, ] 1.0177391 0.9850093 1.0692495 0.9213559 1.0891820 - actual[7, ] 1.0129933 1.0652677 1.1097247 1.0917642 0.9675473 + expected[7, ] 0.9650818 0.9732935 1.0427331 0.9187285 1.0346515 - actual[8, ] 1.0129933 1.0652677 1.1097247 1.0917642 0.9675473 + expected[8, ] 0.9650818 0.9732935 1.0427331 0.9187285 1.0346515 - actual[9, ] 1.1294933 1.0652442 1.0013258 1.0584779 1.0504179 + expected[9, ] 1.0598686 1.0708870 1.0804035 0.9719276 0.9400813 - actual[10, ] 1.1720466 1.1088715 1.0449531 1.1021052 1.0067906 + expected[10, ] 1.0152359 1.0293895 1.0389060 0.9304300 0.9815788 and 183 more ... ── Failure ('test-fays-generalized-replication.R:241:5'): SD2: Same results from conversion vs. creating from scratch ── `conversion_result` (`actual`) not equal to `orig_result` (`expected`). actual vs expected [,1] [,2] [,3] [,4] [,5] - actual[1, ] 1.0782132 1.1618753 0.9856189 0.9602723 1.1076075 + expected[1, ] 0.9803161 1.2294211 1.0585024 0.9416083 1.0178936 - actual[2, ] 1.0782132 1.1618753 0.9856189 0.9602723 1.1076075 + expected[2, ] 0.9803161 1.2294211 1.0585024 0.9416083 1.0178936 - actual[3, ] 0.8959419 0.9540160 0.9853610 0.9730382 0.9124892 + expected[3, ] 1.0433856 0.9142893 0.9519200 1.0480565 0.9504778 - actual[4, ] 0.8959419 0.9540160 0.9853610 0.9730382 0.9124892 + expected[4, ] 1.0433856 0.9142893 0.9519200 1.0480565 0.9504778 - actual[5, ] 1.0577421 0.9104026 0.9449328 1.1064945 0.9955034 + expected[5, ] 0.9957574 0.9129770 0.9439629 1.0202755 1.0287688 - actual[6, ] 1.0577421 0.9104026 0.9449328 1.1064945 0.9955034 + expected[6, ] 0.9957574 0.9129770 0.9439629 1.0202755 1.0287688 - actual[7, ] 1.0052574 1.1331903 1.1684331 0.9577745 1.0386319 + expected[7, ] 0.9642162 1.0947897 1.0861167 0.9962061 0.9879148 - actual[8, ] 1.0052574 1.1331903 1.1684331 0.9577745 1.0386319 + expected[8, ] 0.9642162 1.0947897 1.0861167 0.9962061 0.9879148 - actual[9, ] 0.7809456 0.9891364 0.9272800 1.0573713 0.9261575 + expected[9, ] 0.8581668 0.9910370 0.9204682 1.0324038 1.0380712 - actual[10, ] 0.7809456 0.9891364 0.9272800 1.0573713 0.9261575 + expected[10, ] 0.8581668 0.9910370 0.9204682 1.0324038 1.0380712 and 183 more ... [ FAIL 4 | WARN 0 | SKIP 0 | PASS 209 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [137s/138s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-MKL/svrep.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:03.47, 315.46 + 19.61 ```

For the oldrel macos flavors, CRAN is choking on valid LaTeX...

macos issues ``` using R version 4.2.0 (2022-04-22) using platform: aarch64-apple-darwin20 (64-bit) using session charset: UTF-8 checking for file ‘svrep/DESCRIPTION’ ... OK checking extension type ... Package this is package ‘svrep’ version ‘0.6.1’ package encoding: UTF-8 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 executable files ... OK checking for hidden files and directories ... OK checking for portable file names ... OK checking for sufficient/correct file permissions ... OK checking whether package ‘svrep’ can be installed ... [4s/5s] OK See the [install log](https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/svrep-00install.html) for details. 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 ... OK checking R files for non-ASCII characters ... OK checking R files for syntax errors ... OK 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 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/5s] OK checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK checking data for non-ASCII characters ... OK checking LazyData ... OK checking data for ASCII and uncompressed saves ... OK checking installed files from ‘inst/doc’ ... OK checking files in ‘vignettes’ ... OK checking examples ... [2s/2s] OK checking for unstated dependencies in ‘tests’ ... OK checking tests ... [18s/23s] OK Running ‘testthat.R’ [18s/23s] checking for unstated dependencies in vignettes ... OK checking package vignettes in ‘inst/doc’ ... OK checking running R code from vignettes ... [1s/2s] NONE ‘bootstrap-replicates.Rmd’ using ‘UTF-8’... [0s/1s] OK ‘nonresponse-adjustments.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘sample-based-calibration.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘two-phase-sampling.Rmd’ using ‘UTF-8’... [0s/0s] OK checking re-building of vignette outputs ... [36s/47s] OK checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Misplaced alignment tab character &. w_{i}^{(r)} = \begin {cases} w_{i} & \text {if } i \text { not i... l.1018 }{} ! Undefined control sequence. ...(r)} = \begin {cases} w_{i} & \text {if } i \text { not in var... l.1018 }{} ! Undefined control sequence. ...{cases} w_{i} & \text {if } i \text { not in variance stratum ... l.1018 }{} ! Misplaced alignment tab character &. ...ilde {h} \\ a_{\tilde {h} g} w_{i} & \text {if } i \text { in ... l.1018 }{} ! Undefined control sequence. ...} \\ a_{\tilde {h} g} w_{i} & \text {if } i \text { in } \tild... l.1018 }{} ! Undefined control sequence. ... {h} g} w_{i} & \text {if } i \text { in } \tilde {h} \text { ... l.1018 }{} ! Undefined control sequence. ...f } i \text { in } \tilde {h} \text { but not in random group ... l.1018 }{} ! Misplaced alignment tab character &. ...{ but not in random group } g \\ 0 & \text {if } i \text { in ... l.1018 }{} ! Undefined control sequence. ...ot in random group } g \\ 0 & \text {if } i \text { in random ... l.1018 }{} ! Undefined control sequence. ...roup } g \\ 0 & \text {if } i \text { in random group } g \tex... l.1018 }{} ! Undefined control sequence. ...i \text { in random group } g \text { of } \tilde {h} \\ \end ... l.1018 }{} ! Missing } inserted. } l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! Missing \cr inserted. \cr l.1034 }{} ! Misplaced \cr. \cr l.1034 }{} ! ==> Fatal error occurred, no output PDF file produced! checking PDF version of manual without index ... ERROR DONE Status: 1 ERROR, 1 WARNING using check arguments '--no-clean-on-error ' ```
bschneidr commented 1 year ago

Relevant discussion on the r-help mailing list closely related to this.

https://www.mail-archive.com/r-help@r-project.org/msg267775.html

When using MKL, the same function call can give different results even when using set.seed()... It's not clear how to deal with that.

Update: Here are some StackOverflow discussions about this same problem.

https://stackoverflow.com/questions/20664377/lme-different-results-each-run-under-revolution-r-mkl-to-blame

https://stackoverflow.com/questions/20664377/lme-different-results-each-run-under-revolution-r-mkl-to-blame

bschneidr commented 1 year ago

The following R code was helpful for walking through the UTF-8 checks run by tools::.check_package_datasets(".") to find the troublemaker UTF-8 strings:

```r library(tools) pkgDir <- "." oLC_ct <- Sys.getlocale("LC_CTYPE") on.exit(Sys.setlocale("LC_CTYPE", oLC_ct)) Sys.setlocale("LC_CTYPE", "C") oop <- options(warn = -1) on.exit(options(oop), add = TRUE) check_one <- function(x, ds) { if (!length(x)) return() if (is.list(x)) lapply(unclass(x), check_one, ds = ds) if (is.character(x)) { xx <- unclass(x) enc <- Encoding(xx) latin1 <<- latin1 + sum(enc == "latin1") utf8 <<- utf8 + sum(enc == "UTF-8") if(sum(enc == "UTF-8") > 0) { browser() } bytes <<- bytes + sum(enc == "bytes") unk <- xx[enc == "unknown"] ind <- .Call(tools:::C_check_nonASCII2, unk) if (length(ind)) { non_ASCII <<- c(non_ASCII, unk[ind]) where <<- c(where, rep.int(ds, length(ind))) } } a <- attributes(x) if (!is.null(a)) { lapply(a, check_one, ds = ds) check_one(names(a), ds) } invisible() } files <- tools::list_files_with_type(file.path(pkgDir, "data"), "data") files <- unique(basename(tools::file_path_sans_ext(files))) ans <- vector("list", length(files)) dataEnv <- new.env(hash = TRUE) names(ans) <- files old <- setwd(pkgDir) .try <- function(expr, msg) { oop <- options(warn = 1) on.exit(options(oop)) outConn <- file(open = "w+") sink(outConn, type = "output") sink(outConn, type = "message") tryCatch(withRestarts(withCallingHandlers(expr, error = { function(e) invokeRestart("grmbl", e, sys.calls()) }), grmbl = function(e, calls) { n <- length(sys.calls()) calls <- calls[-seq.int(length.out = n - 1L)] calls <- rev(calls)[-c(1L, 2L)] tb <- lapply(calls, deparse) message(msg, conditionMessage(e), "\nCall sequence:\n", paste(c(utils::head(.eval_with_capture(traceback(tb))$output, 5), " ..."), collapse = "\n"), "\n") }), error = identity, finally = { sink(type = "message") sink(type = "output") close(outConn) }) } for (f in files) { msg <- sprintf("Error loading dataset %s: ", sQuote(f)) .try(utils::data(list = f, package = character(), envir = dataEnv), msg) } setwd(old) non_ASCII <- where <- character() latin1 <- utf8 <- bytes <- 0L for (ds in ls(envir = dataEnv, all.names = TRUE)) { print(ds) if (inherits(suppressWarnings(try(check_one(get(ds, envir = dataEnv), ds), silent = TRUE)), "try-error")) { msg <- sprintf("Error loading dataset %s:\n ", sQuote(ds)) message(msg, geterrmessage()) } } unknown <- unique(cbind(non_ASCII, where)) structure(list(latin1 = latin1, utf8 = utf8, bytes = bytes, unknown = unknown), class = "check_package_datasets") ```
bschneidr commented 1 year ago

Fixed as of version 0.6.3, accepted by CRAN and checks are all passing.