############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GSVA_1.52.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GSVA/DESCRIPTION’ ... OK * this is package ‘GSVA’ version ‘1.52.1’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GSVA’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * 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 code 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 whether startup messages can be suppressed ... 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 ... 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ Running ‘test_gsva_newapi.R’ Comparing ‘test_gsva_newapi.Rout’ to ‘test_gsva_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname 161c161 < KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879766 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736 --- > KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879477 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736 163c163 < KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55050994 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745 --- > KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55049088 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745 166c166 < KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35347309 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262 --- > KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35356594 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262 173c173 < KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257010 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129 --- > KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257184 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129 Running ‘test_plage_newapi.R’ Comparing ‘test_plage_newapi.Rout’ to ‘test_plage_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname 133c133 < KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM -0.08708061 -0.36924639 -0.16317478 0.18733952 0.22969884 0.07403687 -0.005513622 0.13403336 0.10757766 0.11347043 0.126968905 0.068529526 0.073097377 -0.145409314 -0.117559506 -0.192280283 -0.262745324 -0.261030448 0.187064190 0.10806619 0.21446933 -0.264815017 -0.32316348 0.02316450 0.08242710 -0.09121413 0.08115837 0.06082489 -0.05128248 0.096144492 0.1729482337 0.179767986 -0.079378632 -0.2025544282 0.14107384 0.1545868541 --- > KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.08708061 0.36924639 0.16317478 -0.18733952 -0.22969884 -0.07403687 0.005513622 -0.13403336 -0.10757766 -0.11347043 -0.126968905 -0.068529526 -0.073097377 0.145409314 0.117559506 0.192280283 0.262745324 0.261030448 -0.187064190 -0.10806619 -0.21446933 0.264815017 0.32316348 -0.02316450 -0.08242710 0.09121413 -0.08115837 -0.06082489 0.05128248 -0.096144492 -0.1729482337 -0.179767986 0.079378632 0.2025544282 -0.14107384 -0.1545868541 136c136 < KEGG_FATTY_ACID_METABOLISM -0.25246920 -0.21487789 -0.06756412 0.24015561 0.15971798 -0.04164973 0.134634522 -0.18133621 -0.18742246 0.09879733 -0.059789040 -0.211657105 0.189741758 -0.051073442 0.063493728 0.055876110 0.064518498 -0.032865183 -0.144745872 0.12747677 0.34740988 -0.017286592 -0.07659859 0.12250954 0.14145045 0.32332540 0.30311340 -0.30156896 -0.14235300 0.020396100 -0.1491018982 0.054180990 -0.209632783 0.0622606872 -0.15856855 -0.0084981268 --- > KEGG_FATTY_ACID_METABOLISM 0.25246920 0.21487789 0.06756412 -0.24015561 -0.15971798 0.04164973 -0.134634522 0.18133621 0.18742246 -0.09879733 0.059789040 0.211657105 -0.189741758 0.051073442 -0.063493728 -0.055876110 -0.064518498 0.032865183 0.144745872 -0.12747677 -0.34740988 0.017286592 0.07659859 -0.12250954 -0.14145045 -0.32332540 -0.30311340 0.30156896 0.14235300 -0.020396100 0.1491018982 -0.054180990 0.209632783 -0.0622606872 0.15856855 0.0084981268 145c145 < KEGG_CYSTEINE_AND_METHIONINE_METABOLISM -0.14011533 -0.44950137 -0.13715860 0.21286365 0.25951992 -0.03554671 0.035671613 0.01235037 -0.10835898 0.19692749 -0.119707919 -0.229911107 0.124986706 -0.071248763 0.050382477 -0.112207174 0.038781286 -0.141432934 -0.158050492 0.24246930 0.20193494 -0.019331667 -0.10357964 0.11758175 0.13149796 0.30066366 0.23406437 -0.28585381 -0.13769399 -0.074084706 -0.0009278377 0.149035605 -0.067135796 0.0470514419 -0.08543382 0.1214980980 --- > KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.14011533 0.44950137 0.13715860 -0.21286365 -0.25951992 0.03554671 -0.035671613 -0.01235037 0.10835898 -0.19692749 0.119707919 0.229911107 -0.124986706 0.071248763 -0.050382477 0.112207174 -0.038781286 0.141432934 0.158050492 -0.24246930 -0.20193494 0.019331667 0.10357964 -0.11758175 -0.13149796 -0.30066366 -0.23406437 0.28585381 0.13769399 0.074084706 0.0009278377 -0.149035605 0.067135796 -0.0470514419 0.08543382 -0.1214980980 161c161 < KEGG_CITRATE_CYCLE_TCA_CYCLE -0.15203505 0.17111274 -0.0192425535 -0.05927134 -0.10807196 -0.11312140 -0.28808722 -0.12139802 0.4880436 -0.15299104 0.04906447 0.0147576258 -0.0316875534 -0.11937406 -0.0089518864 0.2637738 -0.0406273352 4.893202e-02 -0.0399987391 -0.020132090 -0.24689245 0.14284022 -0.0008861416 0.16483674 0.08846222 0.14421236 -0.18663124 0.3056940 0.10053188 -0.025582990 -0.2761436 0.11072658 0.17974086 -0.2615204 -0.021548560 0.0214665332 --- > KEGG_CITRATE_CYCLE_TCA_CYCLE 0.15203505 -0.17111274 0.0192425535 0.05927134 0.10807196 0.11312140 0.28808722 0.12139802 -0.4880436 0.15299104 -0.04906447 -0.0147576258 0.0316875534 0.11937406 0.0089518864 -0.2637738 0.0406273352 -4.893202e-02 0.0399987391 0.020132090 0.24689245 -0.14284022 0.0008861416 -0.16483674 -0.08846222 -0.14421236 0.18663124 -0.3056940 -0.10053188 0.025582990 0.2761436 -0.11072658 -0.17974086 0.2615204 0.021548560 -0.0214665332 164c164 < KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM -0.11684514 0.15932375 -0.0424584303 -0.08863850 -0.01606414 -0.07687084 -0.26942124 -0.09040454 0.4770715 -0.19043992 0.02814712 -0.0084783419 -0.0113907130 -0.11293532 -0.0081665138 0.2110960 -0.0520711362 -5.324071e-05 -0.0002572043 -0.004341436 -0.20787937 0.14010382 0.0237929613 0.14074488 0.11101353 0.11615857 -0.13347359 0.3440427 0.08201004 -0.014824329 -0.4008495 0.13645213 0.18798271 -0.2656192 -0.001164264 -0.0452927563 --- > KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.11684514 -0.15932375 0.0424584303 0.08863850 0.01606414 0.07687084 0.26942124 0.09040454 -0.4770715 0.19043992 -0.02814712 0.0084783419 0.0113907130 0.11293532 0.0081665138 -0.2110960 0.0520711362 5.324071e-05 0.0002572043 0.004341436 0.20787937 -0.14010382 -0.0237929613 -0.14074488 -0.11101353 -0.11615857 0.13347359 -0.3440427 -0.08201004 0.014824329 0.4008495 -0.13645213 -0.18798271 0.2656192 0.001164264 0.0452927563 167c167 < KEGG_FATTY_ACID_METABOLISM -0.14404628 0.17549826 0.0168733006 -0.03662427 -0.13805007 -0.13510632 -0.29212490 -0.11769787 0.4538781 -0.16997502 0.05292794 0.0171357447 -0.0056091986 -0.20068593 0.0171192068 0.2391582 -0.0523800221 3.355725e-02 0.0037541309 -0.007606301 -0.26720390 0.13680786 0.0229006319 0.12955701 0.16649337 0.18843753 -0.11227260 0.3030089 0.07180728 -0.065746889 -0.3537898 0.09725041 0.16000999 -0.1584219 -0.002131614 -0.0267022633 --- > KEGG_FATTY_ACID_METABOLISM 0.14404628 -0.17549826 -0.0168733006 0.03662427 0.13805007 0.13510632 0.29212490 0.11769787 -0.4538781 0.16997502 -0.05292794 -0.0171357447 0.0056091986 0.20068593 -0.0171192068 -0.2391582 0.0523800221 -3.355725e-02 -0.0037541309 0.007606301 0.26720390 -0.13680786 -0.0229006319 -0.12955701 -0.16649337 -0.18843753 0.11227260 -0.3030089 -0.07180728 0.065746889 0.3537898 -0.09725041 -0.16000999 0.1584219 0.002131614 0.0267022633 174,176c174,176 < KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.16187518 0.15242447 -0.0445845851 -0.03801959 -0.16815027 -0.15816036 -0.18629258 -0.13647099 0.4547896 -0.15764760 0.09834758 0.0673653703 0.0327515803 -0.13813612 0.0001154741 0.2242866 0.0035237558 8.144324e-02 -0.0846143930 -0.016951778 -0.35755319 0.12650621 0.0869564600 0.15472376 0.13565892 0.15047719 -0.19304761 0.2923463 0.10340182 -0.124156397 -0.2929275 0.08529239 0.17347808 -0.1458381 -0.019564617 0.0001020227 < KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM -0.18425567 0.21997777 -0.0792549975 -0.02796617 -0.15066508 -0.13108206 -0.09096202 -0.09603363 0.4087696 -0.19271142 0.11346497 0.0412294265 0.0825276719 -0.25407808 0.0336109990 0.1920607 0.0511250493 1.385250e-01 -0.0965515196 0.005825203 -0.28983157 0.12541010 0.0631413865 0.18063408 -0.07210946 0.15207612 -0.12502562 0.3434555 0.08266163 -0.241050135 -0.2367705 0.13650734 0.16052837 -0.1219852 -0.122337569 -0.0188602175 < KEGG_CYSTEINE_AND_METHIONINE_METABOLISM -0.21582742 0.19257267 -0.0481026570 -0.12532384 -0.12863263 -0.12702487 -0.21916790 -0.14145654 0.4628510 -0.18903573 0.08990904 0.0356654022 0.0293211714 -0.21616290 -0.0113339421 0.2359683 -0.0240081539 8.452455e-02 -0.0615230196 0.031731840 -0.26949610 0.14960573 0.0490440852 0.18626782 0.06807870 0.13588057 -0.13260775 0.3153507 0.07004173 -0.095123437 -0.2314867 0.12190522 0.17317799 -0.1942247 -0.001740289 0.0003819966 --- > KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.16187518 -0.15242447 0.0445845851 0.03801959 0.16815027 0.15816036 0.18629258 0.13647099 -0.4547896 0.15764760 -0.09834758 -0.0673653703 -0.0327515803 0.13813612 -0.0001154741 -0.2242866 -0.0035237558 -8.144324e-02 0.0846143930 0.016951778 0.35755319 -0.12650621 -0.0869564600 -0.15472376 -0.13565892 -0.15047719 0.19304761 -0.2923463 -0.10340182 0.124156397 0.2929275 -0.08529239 -0.17347808 0.1458381 0.019564617 -0.0001020227 > KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.18425567 -0.21997777 0.0792549975 0.02796617 0.15066508 0.13108206 0.09096202 0.09603363 -0.4087696 0.19271142 -0.11346497 -0.0412294265 -0.0825276719 0.25407808 -0.0336109990 -0.1920607 -0.0511250493 -1.385250e-01 0.0965515196 -0.005825203 0.28983157 -0.12541010 -0.0631413865 -0.18063408 0.07210946 -0.15207612 0.12502562 -0.3434555 -0.08266163 0.241050135 0.2367705 -0.13650734 -0.16052837 0.1219852 0.122337569 0.0188602175 > KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.21582742 -0.19257267 0.0481026570 0.12532384 0.12863263 0.12702487 0.21916790 0.14145654 -0.4628510 0.18903573 -0.08990904 -0.0356654022 -0.0293211714 0.21616290 0.0113339421 -0.2359683 0.0240081539 -8.452455e-02 0.0615230196 -0.031731840 0.26949610 -0.14960573 -0.0490440852 -0.18626782 -0.06807870 -0.13588057 0.13260775 -0.3153507 -0.07004173 0.095123437 0.2314867 -0.12190522 -0.17317799 0.1942247 0.001740289 -0.0003819966 184c184 < KEGG_TRYPTOPHAN_METABOLISM -0.17049240 0.19170650 -0.0004630847 -0.05089247 -0.12593277 -0.11515466 -0.27670376 -0.12909756 0.4814202 -0.17977370 0.06320424 0.0194461931 -0.0070929693 -0.19100894 0.0230060896 0.2042648 0.0001048516 7.878183e-02 -0.0931404987 0.026808640 -0.24465868 0.13838085 0.0248749524 0.16243909 0.09741608 0.15878157 -0.07600539 0.2897865 0.09352519 -0.056621625 -0.3530154 0.08401918 0.15938269 -0.2105366 -0.043211634 0.0264526019 --- > KEGG_TRYPTOPHAN_METABOLISM 0.17049240 -0.19170650 0.0004630847 0.05089247 0.12593277 0.11515466 0.27670376 0.12909756 -0.4814202 0.17977370 -0.06320424 -0.0194461931 0.0070929693 0.19100894 -0.0230060896 -0.2042648 -0.0001048516 -7.878183e-02 0.0931404987 -0.026808640 0.24465868 -0.13838085 -0.0248749524 -0.16243909 -0.09741608 -0.15878157 0.07600539 -0.2897865 -0.09352519 0.056621625 0.3530154 -0.08401918 -0.15938269 0.2105366 0.043211634 -0.0264526019 224c224 < LU_TUMOR_VASCULATURE_UP 0.2378969459 0.062771846 0.34031239 -0.168539328 0.005657595 -0.008190157 0.167323313 0.338981975 0.012484156 0.02906254 -7.237425e-02 0.0041181720 -0.05644821 0.09547833 0.17278295 0.026587364 0.15721892 0.08290324 0.07692133 -0.027096635 0.15539443 0.039807725 0.0907044859 -0.15741811 -0.099085419 0.025321125 -0.12258506 -0.194526161 0.21552019 -0.417930079 -0.09449431 -0.15446705 -0.179506032 -2.947411e-01 -0.20435875 -0.153196747 0.067708347 --- > LU_TUMOR_VASCULATURE_UP -0.2378969459 -0.062771846 -0.34031239 0.168539328 -0.005657595 0.008190157 -0.167323313 -0.338981975 -0.012484156 -0.02906254 7.237425e-02 -0.0041181720 0.05644821 -0.09547833 -0.17278295 -0.026587364 -0.15721892 -0.08290324 -0.07692133 0.027096635 -0.15539443 -0.039807725 -0.0907044859 0.15741811 0.099085419 -0.025321125 0.12258506 0.194526161 -0.21552019 0.417930079 0.09449431 0.15446705 0.179506032 2.947411e-01 0.20435875 0.153196747 -0.067708347 Running ‘test_ssgsea_newapi.R’ Comparing ‘test_ssgsea_newapi.Rout’ to ‘test_ssgsea_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname Running ‘test_zscore_newapi.R’ Comparing ‘test_zscore_newapi.Rout’ to ‘test_zscore_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck/00check.log’ for details.