############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GSVA_1.53.24.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GSVA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GSVA/DESCRIPTION’ ... OK * this is package ‘GSVA’ version ‘1.53.24’ * 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 (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * 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, saveRDS, 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 49,80d48 < < Attaching package: 'matrixStats' < < The following objects are masked from 'package:Biobase': < < anyMissing, rowMedians < < < Attaching package: 'MatrixGenerics' < < The following objects are masked from 'package:matrixStats': < < colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, < colCounts, colCummaxs, colCummins, colCumprods, colCumsums, < colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, < colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, < colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, < colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, < colWeightedMeans, colWeightedMedians, colWeightedSds, < colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, < rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, < rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, < rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, < rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, < rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, < rowWeightedMads, rowWeightedMeans, rowWeightedMedians, < rowWeightedSds, rowWeightedVars < < The following object is masked from 'package:Biobase': < < rowMedians < 157a126 > Mapping identifiers between gene sets and feature names 188a158 > Mapping identifiers between gene sets and feature names 191c161 < 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 193c163 < 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 196c166 < 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 203c173 < 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 221,224c191,194 < astrocytic_up -0.3156918 -0.2937402 -0.2063965 -0.5292883 -0.2702871 -0.2951925 -0.3080243 -0.2791101 0.2571098 0.1418085 0.2230911 -0.3259545 -0.3994021 0.1929370 -0.2731874 -0.3506100 -0.2786548 -0.3496684 -0.4234941 -0.2010393 -0.1692462 -0.3554879 -0.3419162 -0.2301639 0.2812783 -0.3925601 0.2209409 -0.2006161 -0.3579496 0.1953883 -0.1407387 0.1861219 -0.2561213 -0.3916661 -0.1440946 -0.3823206 -0.4728368 -0.3614503 -0.2944791 0.2351151 -0.3259772 -0.4381575 -0.3523582 -0.2555805 -0.2946240 -0.3436803 -0.2920232 0.2524274 -0.2586760 -0.2693912 < astroglia_up -0.5224457 -0.5479084 -0.4801835 -0.6302219 -0.4284473 -0.3667797 -0.4840832 -0.4634742 0.2049344 -0.5104214 -0.3899291 -0.3999971 -0.3548265 -0.4704206 0.1580873 -0.2707711 -0.4738317 -0.5142424 -0.4704900 0.3467707 0.1570760 -0.5356721 -0.5165168 -0.5857397 -0.2026668 -0.4465243 -0.1589945 -0.4535824 -0.5662988 -0.4180301 0.1630794 -0.1848755 -0.4780708 -0.1997052 -0.1901138 -0.5245753 -0.4393916 -0.4491062 -0.4955053 0.2673288 -0.3494524 -0.4067868 -0.5152924 0.1718636 -0.3540658 -0.2902309 -0.2849234 -0.2351337 -0.3816317 -0.4109153 < neuronal_up 0.5513835 0.2420314 -0.2599439 -0.1193085 0.5204313 -0.2202996 -0.3640361 0.3104753 0.4272181 -0.1121238 0.6251314 -0.5049285 -0.4809047 -0.3669485 0.2488173 -0.4027978 0.4164555 -0.4711899 -0.1325816 0.2648056 0.4404559 0.2192098 0.4694595 0.1024740 -0.2448158 -0.2382114 0.5827546 -0.3391725 -0.3634389 -0.1307762 0.1935513 -0.3060780 0.3568401 0.5013831 0.6350209 -0.2596621 0.2678205 0.4671552 0.3769846 0.2199098 0.5167764 -0.3561831 0.3582214 0.5485624 0.1838669 -0.3071349 -0.5400220 0.7033831 0.1452037 -0.1876639 < oligodendrocytic_up 0.3496480 0.2622439 0.3413999 0.1879284 0.4777348 0.3653431 -0.1716562 0.2885168 0.3965637 -0.2456288 0.4137655 0.3105192 0.6201319 0.3291954 -0.1414424 0.4077286 -0.2988871 0.2615457 0.4230068 0.2299087 0.3831987 0.1994364 0.4597292 0.2561263 0.5323454 0.4493016 0.5716207 0.3388746 0.4475002 0.2894455 0.3389028 0.4953043 0.3378928 0.5370713 0.4089257 0.5436365 -0.1457722 0.4153329 0.5862875 -0.1770271 0.4850502 -0.1869804 -0.1718963 0.4793221 0.5425333 0.2318472 0.2232685 0.2903072 0.2032267 0.1424904 --- > astrocytic_up -0.3047539 -0.2946860 -0.1834593 -0.5442776 -0.2834175 -0.2788147 -0.3003514 -0.2874994 0.2607199 0.1413387 0.2146940 -0.3180027 -0.4002297 0.1769516 -0.2588480 -0.3482341 -0.2662723 -0.3459269 -0.4173384 -0.1983332 -0.1586231 -0.3486947 -0.3458663 -0.2206452 0.2825297 -0.3877544 0.2093004 -0.2012996 -0.3454799 0.1747717 -0.1457140 0.1895460 -0.2553038 -0.3954264 -0.1289837 -0.3769329 -0.4737155 -0.3632470 -0.3043683 0.2444025 -0.3233087 -0.4249789 -0.3426041 -0.2380239 -0.3075525 -0.3459151 -0.3087816 0.2381330 -0.2643738 -0.2797349 > astroglia_up -0.5149583 -0.5410770 -0.4707559 -0.6113382 -0.4302575 -0.3653708 -0.4790737 -0.4724831 0.2019720 -0.5165498 -0.3810421 -0.4003590 -0.3525063 -0.4778482 0.1594521 -0.2744265 -0.4668132 -0.5181954 -0.4725050 0.3496106 0.1632234 -0.5350220 -0.5062797 -0.5565810 -0.2063866 -0.4462150 -0.1671050 -0.4503466 -0.5630672 -0.4053433 0.1609667 -0.1794776 -0.4755774 -0.2128034 -0.1997192 -0.5332830 -0.4417129 -0.4310179 -0.4982304 0.2722387 -0.3527572 -0.4120461 -0.5092322 0.1534758 -0.3638957 -0.2886322 -0.3058095 -0.2268245 -0.3789481 -0.4199315 > neuronal_up 0.5535049 0.2417091 -0.2419423 -0.1264513 0.5321516 -0.1907802 -0.3594715 0.3119123 0.4301345 -0.1251531 0.6345184 -0.4761376 -0.4777196 -0.3691534 0.2468458 -0.3802419 0.4236358 -0.4473820 -0.1168248 0.2615203 0.4412960 0.2258959 0.4605784 -0.1201504 -0.2601714 -0.2213066 0.5831010 -0.3449359 -0.3518502 0.1186366 0.1916525 -0.3076000 0.3498210 0.4973920 0.6397865 -0.2787217 0.2572456 0.4607110 0.3686673 0.1846618 0.5245801 -0.3509494 0.3513964 0.5454430 0.1606448 -0.2953076 -0.5303268 0.6995543 0.1475983 -0.1844540 > oligodendrocytic_up 0.3317492 0.2491713 0.3353197 0.1965032 0.4766178 0.3696743 0.1739008 0.2837137 0.3965796 -0.2499617 0.4111354 0.3145638 0.6296969 0.3363415 -0.1374640 0.4114245 -0.3041959 0.2647537 0.4139883 0.2318300 0.3873472 0.2032636 0.4537419 0.2660245 0.5308132 0.4464649 0.5707848 0.3329401 0.4571077 0.2958584 0.3318632 0.4968947 0.3523085 0.5364637 0.4087340 0.5468353 -0.1492890 0.4105960 0.5855587 -0.1819342 0.4798445 -0.1856330 -0.1874635 0.4959465 0.5271533 0.2206708 0.2340045 0.2860177 0.1995836 0.1418165 226,229c196,199 < astrocytic_up -0.4391731 -0.3067137 -0.2402360 0.2861336 0.2903123 0.5433336 0.2447227 0.3121176 0.3281190 0.2333959 0.2710493 0.2418768 0.3259242 0.2364106 0.4051781 0.3404535 0.2479334 0.2972586 -0.1256405 0.4144044 0.2385658 0.2020144 -0.2020782 0.2145881 0.2463716 0.1983981 0.2951102 -0.2048568 0.3421165 0.2580072 0.2477511 0.4663431 0.1829345 0.4247773 0.2899481 0.3157407 -0.3950002 0.1766469 0.1590747 0.1452541 0.2426431 0.1230386 0.3709735 0.2269952 0.2201700 0.2492621 0.2406958 0.1982259 0.3690552 0.3161603 < astroglia_up -0.5563883 -0.2962746 -0.4903974 0.3556835 -0.2043731 0.2495720 -0.2045700 0.2926014 -0.1644211 0.2224271 -0.4686137 -0.1639850 -0.4332908 -0.1756209 -0.2350955 0.2316366 -0.2647208 -0.1687645 -0.4875014 -0.3370291 0.1949577 -0.1472950 -0.2108664 -0.2886618 -0.3116900 -0.2326063 0.2846068 -0.2798815 0.1730262 -0.1742560 -0.3399716 -0.2766437 -0.3094179 0.3760860 0.2280075 0.1525475 -0.2358881 0.4564395 -0.1918375 -0.3070098 -0.2074152 0.3616338 0.2925643 0.3286463 0.1988927 0.1481209 -0.2262431 -0.2227864 -0.2226100 -0.2982872 < neuronal_up 0.2174766 0.1659719 0.4578210 0.5644182 -0.3991141 0.4944911 0.3355468 0.7120803 0.4934655 0.3940480 0.7605592 0.5334811 0.8003920 0.2943079 0.3355093 0.6444976 -0.2226335 0.4704255 0.7153316 0.1947751 0.1546610 0.4909979 0.5875767 -0.1623700 0.7318758 0.5930146 0.3139701 0.4349229 0.2120439 0.1719695 -0.5956769 0.5019625 -0.5806570 0.6560856 0.2674318 -0.5459099 -0.5523664 -0.5491483 0.1299583 -0.1759984 0.1375752 -0.2517609 -0.1897585 -0.3710756 -0.4797184 0.2760896 -0.2042675 -0.6243927 -0.2069522 0.4224564 < oligodendrocytic_up 0.3733027 0.3081813 0.3714361 -0.2050697 -0.4696685 0.1827135 0.2151677 0.3929539 -0.1637416 0.2367050 0.2759246 -0.1864826 0.2537645 0.2863431 -0.1841584 0.3729172 -0.3374760 -0.2654290 -0.2141607 -0.1676218 0.4807783 0.1701692 -0.2325266 -0.1890855 0.3283718 -0.3789054 -0.2422271 -0.4699499 -0.4538349 -0.2799365 -0.3644740 0.2083981 -0.3699899 -0.3345400 0.2371160 0.2762801 -0.3651977 0.1932783 -0.4461610 -0.3465373 -0.3576355 -0.2689566 -0.3662635 -0.3787924 -0.3262132 -0.3081043 -0.2133763 -0.2786529 -0.1809861 0.1315228 --- > astrocytic_up -0.4388712 -0.2984390 -0.2418500 0.2967027 0.2963262 0.5497730 0.2387450 0.3144786 0.3333460 0.2297994 0.2686543 0.2357884 0.3223822 0.2434233 0.4129700 0.3558037 0.2586949 0.2957692 -0.1293295 0.4002767 0.2431737 0.2064763 -0.2054680 0.2098025 0.2378884 0.1979041 0.2823311 0.1955658 0.3445508 0.2594091 0.2529872 0.4826020 0.1815513 0.4318795 0.2885936 0.3123410 -0.3779783 0.1939708 0.1641413 0.1497425 0.2281183 0.1198567 0.3737903 0.2232357 0.2131509 0.2635626 0.2295927 0.2025863 0.3654367 0.3070467 > astroglia_up -0.5577897 -0.3009622 -0.4952939 0.3562099 -0.1948617 0.2506709 -0.1956322 0.2980680 0.1473354 0.1866536 -0.4623550 -0.1714237 -0.4221490 -0.1818365 -0.2457673 0.2500337 -0.2661463 -0.1506672 -0.4899183 -0.3467717 0.2013752 -0.1561121 -0.2157769 -0.2982904 -0.3172812 -0.2281312 0.2970433 -0.2815591 0.1634429 -0.1746780 -0.3294734 -0.2707020 -0.3002505 0.3839744 0.2305549 -0.1605050 -0.2294543 0.4619706 -0.1943197 -0.2982120 -0.2123044 0.3634887 0.2863492 0.3384878 0.1948430 0.1395315 -0.2248029 -0.2162429 -0.2067516 -0.3013420 > neuronal_up 0.2111547 0.1714030 0.4657383 0.5497687 -0.3946098 0.4963120 0.3352992 0.7175166 0.4972767 0.3710156 0.7631191 0.5344811 0.7969773 0.2856497 0.3129090 0.6442165 -0.2297751 0.4688783 0.7186127 0.1864052 0.1512623 0.4905083 0.5779253 -0.1747120 0.7386962 0.5896950 0.2983598 0.4279023 0.2145936 0.1761452 -0.5754318 0.4795529 -0.6007193 0.6585229 0.2712467 -0.5609244 -0.5409766 -0.5582310 -0.1397818 -0.1699394 0.1369626 -0.2852583 -0.2074379 -0.3609699 -0.4746596 0.2723624 -0.1921239 -0.6249382 -0.1989687 0.4172576 > oligodendrocytic_up 0.3666431 0.3008428 0.3834914 -0.2197493 -0.4632601 0.1755629 0.2283133 0.3855686 -0.1581432 0.2212679 0.2711446 -0.1950745 0.2557408 0.2960432 -0.1573391 0.3797065 -0.3338795 -0.2831008 -0.2227159 -0.1671839 0.4939055 0.1723784 -0.2516605 -0.1981382 0.3178961 -0.3937384 -0.2466558 -0.4638286 -0.4636637 -0.2714250 -0.3701235 0.2071280 -0.3779293 -0.3386804 0.2197589 0.2601284 -0.3611962 0.1908298 -0.4231171 -0.3430255 -0.3512123 -0.2820085 -0.3780724 -0.3704518 -0.3216412 -0.3171512 -0.2142009 -0.2771720 -0.1908734 -0.1300848 231,234c201,204 < astrocytic_up 0.4124288 0.3354855 0.2136633 0.2126482 0.2564977 -0.1715118 0.3025815 0.2166845 0.4098713 0.4383413 0.2120418 0.3509768 0.2122194 0.4074719 0.3653733 0.2977469 0.3597309 0.4879931 -0.2911071 0.2820668 -0.2060130 -0.2408318 -0.2865518 0.3965512 -0.2760579 -0.1735798 -0.2717248 0.1608924 0.2062292 -0.2298344 0.1758219 -0.2140975 -0.2486376 0.1518981 0.1552744 0.3899234 0.2294323 0.1192590 -0.2485416 0.18464292 0.1518002 -0.3788665 -0.2714678 0.1961444 -0.1614948 0.3203043 0.2862387 0.2837483 0.2001398 -0.1488755 < astroglia_up -0.3205989 -0.2526287 0.3857193 0.2273568 -0.4587854 -0.2830126 0.2730350 0.3685838 0.3037747 -0.2373707 0.1927742 -0.3176063 0.1807306 0.1766114 0.2551358 0.2093327 -0.2579454 0.3592690 0.4831889 0.2828615 0.5501070 0.4641645 0.5491523 0.5314094 0.3354977 0.2226506 0.5176986 0.4354544 0.4629955 0.3212917 0.5041297 0.4237368 0.3427791 0.4360975 0.3487098 0.5406864 0.5529564 0.3739574 0.4661159 0.35160580 0.4267049 0.4479164 0.4566565 0.3415565 0.4505281 0.3590520 0.3076724 0.5450388 0.4563094 0.2950561 < neuronal_up 0.4856763 -0.5709968 -0.2022545 -0.6120422 0.3580928 -0.4866054 -0.3813493 -0.3257647 0.3998890 0.3034781 0.1441665 -0.5534711 0.4867106 -0.5109675 -0.5810452 -0.3584568 -0.4779479 -0.4197372 -0.3453621 -0.2091667 -0.1638899 -0.5485749 -0.3441300 0.4265041 -0.2017463 -0.2712775 0.2200403 0.1746310 -0.5961173 -0.4496462 0.4943813 0.6670104 -0.4353482 -0.2601941 -0.4179161 -0.2176823 -0.1564704 0.4746688 -0.3404009 -0.38792277 -0.3144457 -0.3933486 -0.4615546 -0.4254415 -0.4028865 -0.3490582 -0.3199808 -0.4385086 -0.4451874 0.3023979 < oligodendrocytic_up -0.2300436 -0.3760417 -0.4069418 -0.4192462 -0.4213447 -0.4945737 -0.2974521 -0.2516607 -0.4520191 -0.3455632 -0.2018836 -0.2199475 -0.4385801 -0.4715313 -0.4262926 -0.4357655 -0.4636387 0.6087937 -0.3988876 -0.1750711 0.1373493 -0.3407164 0.2172557 -0.1937840 -0.4300786 -0.3369981 -0.3652693 -0.3811715 -0.2523106 -0.2933859 0.2439177 0.4972274 -0.3735968 -0.2590977 -0.4025453 0.1536134 0.2356566 0.2644948 0.6288863 0.09236588 -0.3149750 -0.2628590 0.1672503 0.3378009 0.2511021 -0.4467242 -0.2445744 -0.4693471 0.2639368 0.1899161 --- > astrocytic_up 0.4009205 0.3415409 0.2219087 0.2208367 0.2603907 -0.1765010 0.2940235 0.2124375 0.4061779 0.4328053 0.2173015 0.3551808 0.2219615 0.4042258 0.3642527 0.3044645 0.3551091 0.4812290 -0.2947330 0.2717050 -0.2072296 -0.2471975 -0.2842497 0.3991259 -0.2766075 -0.1677575 -0.2641184 -0.1595722 0.1984901 -0.2226697 0.1713801 -0.2188904 -0.2579632 0.1518073 0.1637208 0.3756718 0.2550845 0.1295303 -0.2700193 0.2063444 0.1624008 -0.3704812 -0.2729261 0.1962416 -0.1590410 0.3119768 0.2627011 0.2888753 0.2002931 -0.1400612 > astroglia_up -0.2684818 -0.2478927 0.4042948 0.2335354 -0.4561683 -0.2852517 0.2751976 0.3726306 0.3118150 -0.2394383 0.1820660 -0.2988110 0.1652119 0.1841336 0.2581383 0.2056429 -0.2597831 0.3690882 0.4820315 0.2887467 0.5403445 0.4579650 0.5444281 0.5331769 0.3394440 0.2194871 0.5238034 0.4465451 0.4552118 0.3171873 0.5092584 0.4264341 0.3355302 0.4395682 0.3572217 0.5354133 0.5529363 0.3635790 0.4608111 0.3641927 0.4291813 0.4496740 0.4566347 0.3510896 0.4412179 0.3601076 0.3276640 0.5528990 0.4514321 0.2932687 > neuronal_up 0.4714021 -0.5453959 -0.2184275 -0.6205832 0.3765956 -0.4810052 -0.3898214 -0.3376351 0.4026263 0.2958724 0.1514880 -0.5448607 0.4816556 -0.5156220 -0.5857302 -0.3912544 -0.4810045 -0.4432014 -0.3401462 -0.2069768 -0.1755817 -0.5429475 -0.3473447 0.4293285 -0.1852551 -0.2807897 0.2095081 0.1692813 -0.5953110 -0.4569613 0.4986510 0.6780347 -0.4361162 -0.2657947 -0.4149003 -0.2019748 -0.1825776 0.4705841 -0.3660470 -0.3950770 -0.2875748 -0.3687514 -0.4339034 -0.4137328 -0.4061838 -0.3665761 -0.2886278 -0.4494102 -0.4614783 0.3012511 > oligodendrocytic_up -0.2170210 -0.3505377 -0.4033821 -0.4180423 -0.4282208 -0.4921075 -0.3129745 -0.2568446 -0.4508574 -0.3521717 -0.1932037 -0.2401757 -0.4705363 -0.4756500 -0.3939968 -0.4508653 -0.4673510 0.6267838 -0.3869379 -0.1753464 0.1398180 -0.3356724 0.2174792 -0.1909474 -0.4170448 -0.3449788 -0.3789635 -0.3723979 -0.2489271 -0.2955629 0.2563263 0.5062260 -0.3722382 -0.2544347 -0.4120718 0.1481816 0.2266027 0.2624142 0.6390087 0.1041047 -0.3246204 -0.2504649 0.1695500 0.3362893 0.2602318 -0.4512150 -0.2275365 -0.4490874 0.2728064 0.1801245 236,239c206,209 < astrocytic_up -0.3209234 0.2820414 0.2253645 0.2086038 0.2460212 -0.2336249 -0.3504830 -0.4070533 0.3396053 0.2283260 -0.2674171 0.1111060 -0.2303429 0.1920686 -0.2014208 -0.1522004 -0.2602901 0.1889432 -0.1951221 0.2556293 -0.3889742 -0.3105364 0.1582133 < astroglia_up 0.3895576 0.2658367 0.4720393 0.5745617 0.4816561 0.3800850 0.3666714 0.2355577 0.4749856 0.3929248 0.4419080 0.5576349 0.4804379 0.5026222 0.5419921 0.3606262 0.3070343 0.2825392 0.2823171 0.5497362 0.4000951 0.4390331 0.4022042 < neuronal_up -0.4238401 -0.3141708 -0.2663458 -0.4256802 -0.3680283 -0.3534850 -0.3539926 -0.3480500 -0.2957946 -0.5752968 -0.2725662 0.3014634 -0.3318476 0.6270101 -0.4862421 0.5148910 0.1333564 0.2564390 -0.5179771 -0.3933461 -0.3821281 -0.4576934 -0.2698085 < oligodendrocytic_up -0.1655520 0.2844661 -0.4317947 -0.2081775 -0.4322990 -0.4325976 -0.1254650 -0.2752508 -0.3948615 -0.3803124 -0.2041191 -0.1477494 0.2354539 -0.2838837 -0.2387368 0.2034906 -0.3192081 -0.3323391 -0.2653002 -0.4812430 -0.4455111 -0.4181155 0.1632773 --- > astrocytic_up -0.3141722 0.2699874 0.2219473 0.2091188 0.2345999 -0.2194917 -0.3453076 -0.4238358 0.3549822 0.2340566 -0.2593196 0.1099604 -0.2273672 0.2019316 -0.2041700 -0.1508235 -0.2519564 0.1867464 -0.1965190 0.2585439 -0.3990271 -0.3061357 0.1651281 > astroglia_up 0.3922137 0.2846455 0.4656351 0.5682138 0.4886159 0.3895400 0.3730679 0.2343013 0.4820948 0.3943550 0.4396104 0.5514612 0.4772503 0.5054087 0.5478562 0.3711037 0.3050986 0.2872253 0.2808018 0.5497252 0.4051805 0.4516472 0.4085658 > neuronal_up -0.4367833 -0.3295978 -0.2846818 -0.4517050 -0.3885191 -0.3608320 -0.3779686 -0.3484378 -0.2868552 -0.5719856 -0.2625708 0.2935293 -0.3335214 0.6340333 -0.4788773 0.5079833 0.1255322 0.2449831 -0.5029271 -0.3891953 -0.3632664 -0.4659142 -0.2670667 > oligodendrocytic_up -0.1680797 0.2981662 -0.4332569 -0.2097164 -0.4411032 -0.4515751 -0.1344606 -0.2894701 -0.3966829 -0.3681011 -0.2038674 -0.1537039 0.2336640 -0.2932406 -0.2495044 0.2091980 -0.3179201 -0.3245650 -0.2703005 -0.4534530 -0.4265475 -0.4192150 0.1600080 245a216 > Mapping identifiers between gene sets and feature names 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, saveRDS, 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 49,80d48 < < Attaching package: 'matrixStats' < < The following objects are masked from 'package:Biobase': < < anyMissing, rowMedians < < < Attaching package: 'MatrixGenerics' < < The following objects are masked from 'package:matrixStats': < < colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, < colCounts, colCummaxs, colCummins, colCumprods, colCumsums, < colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, < colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, < colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, < colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, < colWeightedMeans, colWeightedMedians, colWeightedSds, < colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, < rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, < rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, < rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, < rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, < rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, < rowWeightedMads, rowWeightedMeans, rowWeightedMedians, < rowWeightedSds, rowWeightedVars < < The following object is masked from 'package:Biobase': < < rowMedians < 157a126 > Mapping identifiers between gene sets and feature names 187a157 > Mapping identifiers between gene sets and feature names 244a215 > Mapping identifiers between gene sets and feature names 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, saveRDS, 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 49,80d48 < < Attaching package: 'matrixStats' < < The following objects are masked from 'package:Biobase': < < anyMissing, rowMedians < < < Attaching package: 'MatrixGenerics' < < The following objects are masked from 'package:matrixStats': < < colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, < colCounts, colCummaxs, colCummins, colCumprods, colCumsums, < colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, < colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, < colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, < colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, < colWeightedMeans, colWeightedMedians, colWeightedSds, < colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, < rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, < rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, < rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, < rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, < rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, < rowWeightedMads, rowWeightedMeans, rowWeightedMedians, < rowWeightedSds, rowWeightedVars < < The following object is masked from 'package:Biobase': < < rowMedians < 111,113c79,81 < ℹ Calculating ranks < ℹ Calculating rank weights < ℹ Normalizing ssGSEA scores --- > [1] "Calculating ranks..." > [1] "Calculating absolute values from ranks..." > [1] "Normalizing..." 161,163c129,132 < ℹ Calculating ranks < ℹ Calculating rank weights < ℹ Normalizing ssGSEA scores --- > Mapping identifiers between gene sets and feature names > [1] "Calculating ranks..." > [1] "Calculating absolute values from ranks..." > [1] "Normalizing..." 194,196c163,166 < ℹ Calculating ranks < ℹ Calculating rank weights < ℹ Normalizing ssGSEA scores --- > Mapping identifiers between gene sets and feature names > [1] "Calculating ranks..." > [1] "Calculating absolute values from ranks..." > [1] "Normalizing..." 227,229c197,199 < ℹ Calculating ranks < ℹ Calculating rank weights < ℹ Normalizing ssGSEA scores --- > [1] "Calculating ranks..." > [1] "Calculating absolute values from ranks..." > [1] "Normalizing..." 257,259c227,230 < ℹ Calculating ranks < ℹ Calculating rank weights < ℹ Normalizing ssGSEA scores --- > Mapping identifiers between gene sets and feature names > [1] "Calculating ranks..." > [1] "Calculating absolute values from ranks..." > [1] "Normalizing..." 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, saveRDS, 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 49,80d48 < < Attaching package: 'matrixStats' < < The following objects are masked from 'package:Biobase': < < anyMissing, rowMedians < < < Attaching package: 'MatrixGenerics' < < The following objects are masked from 'package:matrixStats': < < colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, < colCounts, colCummaxs, colCummins, colCumprods, colCumsums, < colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, < colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, < colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, < colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, < colWeightedMeans, colWeightedMedians, colWeightedSds, < colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, < rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, < rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, < rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, < rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, < rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, < rowWeightedMads, rowWeightedMeans, rowWeightedMedians, < rowWeightedSds, rowWeightedVars < < The following object is masked from 'package:Biobase': < < rowMedians < 157a126 > Mapping identifiers between gene sets and feature names 187a157 > Mapping identifiers between gene sets and feature names 244a215 > Mapping identifiers between gene sets and feature names OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GSVA.Rcheck/00check.log’ for details.