* using log directory 'd:/Rcompile/CRANpkg/local/4.4/demic.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'demic/DESCRIPTION' ... OK * this is package 'demic' version '2.0.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'demic' can be installed ... OK * checking installed package size ... OK * checking package 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [2s] OK * checking loading without being on the library search path ... [2s] 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 ... [6s] OK * checking Rd files ... [1s] 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 ... [1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [18s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [23s] ERROR Running 'testthat.R' [23s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(demic) > > test_check("demic") $all_ptr est_ptr coefficient pValue cor correctY Akk0_001 1.946931 0.3840328 7.840437e-25 0.9970041 3.260867 Akk1_001 2.763177 0.5858478 1.476701e-26 0.9979485 3.321042 Akk2_001 3.449088 0.7136534 5.229909e-31 0.9992274 3.361187 $contigs_ptr est_ptr coefficient pValue cor correctY Akk0_001 1.902701 0.3876469 1.123509e-15 0.9971278 3.297423 Akk1_001 2.647933 0.5864348 6.691953e-16 0.9982519 3.377764 Akk2_001 3.259171 0.7112131 8.908332e-20 0.9993580 3.416064 $samples_ptr NULL est_ptr coefficient pValue cor correctY Bfrag0_002 2.061760 0.3699599 1.470163e-36 0.9918912 2.216383 Bfrag1_002 3.043483 0.5690839 3.576654e-49 0.9981767 2.222179 Bfrag2_002 4.204818 0.7343522 1.049070e-51 0.9986483 2.208119 est_ptr coefficient pValue cor correctY Ecoli0_003 1.793911 0.3811338 8.281071e-20 0.9837530 2.391533 Ecoli1_003 2.412955 0.5752038 4.556634e-27 0.9950547 2.370112 Ecoli2_003 3.099395 0.7236211 2.210400e-25 0.9952108 2.335064 $all_ptr est_ptr coefficient pValue cor correctY Sample1 1.577167 0.3978371 8.111920e-37 0.7637339 1.481230 Sample2 2.354320 0.7476431 1.453821e-88 0.9410749 1.588319 Sample3 1.838580 0.5317476 1.621567e-46 0.8202775 1.417947 $contigs_ptr est_ptr coefficient pValue cor correctY Sample1 1.526259 0.3937088 2.839010e-22 0.7396687 1.477589 Sample2 2.222795 0.7436559 3.133542e-54 0.9330790 1.549798 Sample3 1.787794 0.5402733 3.868121e-28 0.8098274 1.419747 $samples_ptr NULL $all_ptr est_ptr coefficient pValue cor correctY Sample1 2.281308 0.6319368 5.251404e-62 0.9775760 0.3235725 Sample2 1.748664 0.4282018 4.980528e-39 0.9244302 0.3799434 Sample3 2.323527 0.6459869 1.588855e-64 0.9803428 0.3075130 $contigs_ptr est_ptr coefficient pValue cor correctY Sample1 2.042897 0.6447588 1.253119e-27 0.9726712 0.4397235 Sample2 1.600614 0.4167767 3.125277e-13 0.8887421 0.4204469 Sample3 2.036625 0.6401553 5.029860e-30 0.9772943 0.4083257 $samples_ptr NULL structure(list(`(Intercept)` = c(0.122133753095513, 0.112468233560288, 0.0372788404325122, 0.177304339887256, 0.0270507610681736, 0.0842232868459067, 0.106812647682803, 0.162034499737329, 0.14194349045613, 0.138951868657145 ), GC_content = c(-0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212, -0.139377848208212), s_c = c("a:1", "a:2", "b:3", "b:4", "c:5", "c:6", "d:7", "d:8", "e:9", "e:10")), row.names = c("a:1", "a:2", "b:3", "b:4", "c:5", "c:6", "d:7", "d:8", "e:9", "e:10"), class = "data.frame") [ FAIL 1 | WARN 9 | SKIP 0 | PASS 42 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-est_ptr.R:48:3'): DEMIC main function produces correct output on sourceforge data cluster 2 ── O$contigs_ptr (`actual`) not equal to `EO2` (`expected`). actual vs expected correctY - actual[1, ] 0.4397235 + expected[1, ] 0.3099378 - actual[2, ] 0.4204469 + expected[2, ] 0.3779174 - actual[3, ] 0.4083257 + expected[3, ] 0.3044411 `actual$correctY`: 0.4 0.4 0.4 `expected$correctY`: 0.3 0.4 0.3 [ FAIL 1 | WARN 9 | SKIP 0 | PASS 42 ] Error: Test failures Execution halted * checking PDF version of manual ... [22s] OK * checking HTML version of manual ... [4s] OK * DONE Status: 1 ERROR