############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:partCNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings partCNV_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/partCNV.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘partCNV/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘partCNV’ version ‘1.2.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘partCNV’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... 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 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 ... NOTE GetCytoLocation: no visible global function definition for ‘data’ GetExprCountCyto: no visible global function definition for ‘data’ Undefined global functions or variables: data Consider adding importFrom("utils", "data") to your NAMESPACE file. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘partCNV-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GetCytoLocation > ### Title: Get exact location of the interested cytogenetics feature > ### Aliases: GetCytoLocation > > ### ** Examples > > ### example 1 > GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") downloading 1 resources retrieving 1 resource loading from cache require(“GenomicRanges”) Interested region: chr20:28100001-51200000. A total of 381 genes are located in this region. $chr_location [1] "chr20" $cyto_start [1] 28100001 $cyto_end [1] 51200000 $overGeneID [1] "ENSG00000287889" "ENSG00000205611" "ENSG00000286483" "ENSG00000287288" [5] "ENSG00000231934" "ENSG00000215547" "ENSG00000215545" "ENSG00000131068" [9] "ENSG00000180483" "ENSG00000204548" "ENSG00000180424" "ENSG00000180383" [13] "ENSG00000088320" "ENSG00000233354" "ENSG00000101294" "ENSG00000274364" [17] "ENSG00000101898" "ENSG00000235313" "ENSG00000230613" "ENSG00000278276" [21] "ENSG00000125968" "ENSG00000131055" "ENSG00000171552" "ENSG00000236559" [25] "ENSG00000281376" "ENSG00000088325" "ENSG00000101306" "ENSG00000179772" [29] "ENSG00000149599" "ENSG00000131044" "ENSG00000088356" "ENSG00000260903" [33] "ENSG00000278012" "ENSG00000226239" "ENSG00000101331" "ENSG00000101336" [37] "ENSG00000101337" "ENSG00000275576" "ENSG00000126003" "ENSG00000101346" [41] "ENSG00000287850" "ENSG00000101350" "ENSG00000277692" "ENSG00000171456" [45] "ENSG00000197183" "ENSG00000236772" "ENSG00000286311" "ENSG00000277301" [49] "ENSG00000233293" "ENSG00000204393" "ENSG00000228156" "ENSG00000198547" [53] "ENSG00000149600" "ENSG00000088305" "ENSG00000101367" "ENSG00000260536" [57] "ENSG00000260257" "ENSG00000215529" "ENSG00000167098" "ENSG00000078898" [61] "ENSG00000167104" "ENSG00000186190" "ENSG00000186191" "ENSG00000131050" [65] "ENSG00000224876" "ENSG00000131059" "ENSG00000198183" "ENSG00000125999" [69] "ENSG00000101391" "ENSG00000101400" "ENSG00000078699" "ENSG00000275223" [73] "ENSG00000125967" "ENSG00000149609" "ENSG00000182584" "ENSG00000271803" [77] "ENSG00000101412" "ENSG00000101417" "ENSG00000229188" "ENSG00000131061" [81] "ENSG00000230753" "ENSG00000101421" "ENSG00000285230" "ENSG00000125970" [85] "ENSG00000228386" "ENSG00000125977" "ENSG00000287853" "ENSG00000101440" [89] "ENSG00000250917" "ENSG00000101444" "ENSG00000272945" "ENSG00000078747" [93] "ENSG00000236388" "ENSG00000231795" "ENSG00000277558" "ENSG00000125971" [97] "ENSG00000101460" "ENSG00000101464" "ENSG00000198646" "ENSG00000078804" [101] "ENSG00000286803" "ENSG00000131067" "ENSG00000131069" "ENSG00000100983" [105] "ENSG00000078814" "ENSG00000100991" "ENSG00000088298" "ENSG00000101000" [109] "ENSG00000278367" "ENSG00000126005" "ENSG00000125966" "ENSG00000242372" [113] "ENSG00000235214" "ENSG00000125998" "ENSG00000101019" "ENSG00000204183" [117] "ENSG00000125965" "ENSG00000126001" "ENSG00000230155" "ENSG00000125975" [121] "ENSG00000125991" "ENSG00000061656" "ENSG00000214078" "ENSG00000244462" [125] "ENSG00000244005" "ENSG00000125995" "ENSG00000131051" "ENSG00000025293" [129] "ENSG00000171222" "ENSG00000149646" "ENSG00000260032" "ENSG00000234139" [133] "ENSG00000277235" "ENSG00000237063" "ENSG00000088367" "ENSG00000232406" [137] "ENSG00000278035" "ENSG00000131043" "ENSG00000080845" "ENSG00000232907" [141] "ENSG00000101335" "ENSG00000118707" "ENSG00000101084" "ENSG00000101082" [145] "ENSG00000101079" "ENSG00000149636" "ENSG00000149639" "ENSG00000101342" [149] "ENSG00000101347" "ENSG00000080839" "ENSG00000269846" "ENSG00000101353" [153] "ENSG00000118705" "ENSG00000118702" "ENSG00000101363" "ENSG00000286240" [157] "ENSG00000197122" "ENSG00000166619" "ENSG00000053438" "ENSG00000276603" [161] "ENSG00000274469" "ENSG00000225759" "ENSG00000204117" "ENSG00000132792" [165] "ENSG00000132821" "ENSG00000101407" "ENSG00000101413" "ENSG00000277550" [169] "ENSG00000198959" "ENSG00000149633" "ENSG00000277829" "ENSG00000285347" [173] "ENSG00000285100" "ENSG00000206249" "ENSG00000101425" "ENSG00000129988" [177] "ENSG00000275285" "ENSG00000224635" "ENSG00000275401" "ENSG00000196756" [181] "ENSG00000174365" "ENSG00000170471" "ENSG00000182035" "ENSG00000124143" [185] "ENSG00000101438" "ENSG00000101442" "ENSG00000101445" "ENSG00000101447" [189] "ENSG00000274825" "ENSG00000261431" "ENSG00000101452" "ENSG00000277581" [193] "ENSG00000230324" "ENSG00000287983" "ENSG00000286083" "ENSG00000229976" [197] "ENSG00000237767" "ENSG00000233415" "ENSG00000223410" "ENSG00000204103" [201] "ENSG00000229771" "ENSG00000286972" "ENSG00000198900" "ENSG00000226648" [205] "ENSG00000124181" "ENSG00000174306" "ENSG00000132793" "ENSG00000183798" [209] "ENSG00000124177" "ENSG00000273951" "ENSG00000225458" "ENSG00000228959" [213] "ENSG00000196090" "ENSG00000229042" "ENSG00000227599" "ENSG00000233508" [217] "ENSG00000124193" "ENSG00000185513" "ENSG00000226143" "ENSG00000101049" [221] "ENSG00000282876" "ENSG00000101052" "ENSG00000101057" "ENSG00000124196" [225] "ENSG00000233277" "ENSG00000124191" "ENSG00000149596" "ENSG00000287570" [229] "ENSG00000132823" "ENSG00000223891" "ENSG00000124194" "ENSG00000197296" [233] "ENSG00000101074" "ENSG00000226812" "ENSG00000101076" "ENSG00000229005" [237] "ENSG00000233376" "ENSG00000168746" "ENSG00000124120" "ENSG00000132824" [241] "ENSG00000168734" "ENSG00000196839" "ENSG00000283440" "ENSG00000244558" [245] "ENSG00000064205" "ENSG00000124249" "ENSG00000276223" "ENSG00000101098" [249] "ENSG00000286100" "ENSG00000166913" "ENSG00000101104" "ENSG00000025772" [253] "ENSG00000227477" "ENSG00000101109" "ENSG00000124134" "ENSG00000175121" [257] "ENSG00000168703" "ENSG00000124102" "ENSG00000124233" "ENSG00000124157" [261] "ENSG00000124107" "ENSG00000124159" "ENSG00000124232" "ENSG00000124145" [265] "ENSG00000275894" "ENSG00000204070" "ENSG00000124251" "ENSG00000244274" [269] "ENSG00000124155" "ENSG00000277022" "ENSG00000101443" "ENSG00000237464" [273] "ENSG00000101446" "ENSG00000243543" "ENSG00000101448" "ENSG00000158901" [277] "ENSG00000180205" "ENSG00000180305" "ENSG00000180083" "ENSG00000182931" [281] "ENSG00000168634" "ENSG00000149651" "ENSG00000124116" "ENSG00000101457" [285] "ENSG00000175063" "ENSG00000101470" "ENSG00000124104" "ENSG00000101473" [289] "ENSG00000132801" "ENSG00000168612" "ENSG00000149634" "ENSG00000124257" [293] "ENSG00000064601" "ENSG00000271984" "ENSG00000100979" "ENSG00000285796" [297] "ENSG00000100982" "ENSG00000198026" "ENSG00000100985" "ENSG00000204044" [301] "ENSG00000124140" "ENSG00000124160" "ENSG00000101017" "ENSG00000229957" [305] "ENSG00000149654" "ENSG00000080189" "ENSG00000273828" "ENSG00000062598" [309] "ENSG00000198185" "ENSG00000149635" "ENSG00000158296" "ENSG00000273893" [313] "ENSG00000172315" "ENSG00000271784" "ENSG00000197496" "ENSG00000064655" [317] "ENSG00000236028" "ENSG00000101040" "ENSG00000267882" "ENSG00000273451" [321] "ENSG00000231119" "ENSG00000224565" "ENSG00000124151" "ENSG00000196562" [325] "ENSG00000255438" "ENSG00000234967" "ENSG00000228503" "ENSG00000287443" [329] "ENSG00000237423" "ENSG00000229522" "ENSG00000286179" "ENSG00000287335" [333] "ENSG00000276923" "ENSG00000287107" "ENSG00000288083" "ENSG00000286063" [337] "ENSG00000235621" "ENSG00000236874" "ENSG00000274261" "ENSG00000281365" [341] "ENSG00000281460" "ENSG00000124126" "ENSG00000286159" "ENSG00000278231" [345] "ENSG00000124198" "ENSG00000227431" "ENSG00000124207" "ENSG00000124214" [349] "ENSG00000124228" "ENSG00000124201" "ENSG00000177410" "ENSG00000158445" [353] "ENSG00000124212" "ENSG00000158470" "ENSG00000197818" "ENSG00000158480" [357] "ENSG00000124226" "ENSG00000124216" "ENSG00000231265" "ENSG00000244687" [361] "ENSG00000240849" "ENSG00000237595" "ENSG00000234698" "ENSG00000231742" [365] "ENSG00000277449" "ENSG00000172216" "ENSG00000224397" "ENSG00000203999" [369] "ENSG00000233077" "ENSG00000196396" "ENSG00000232043" "ENSG00000042062" [373] "ENSG00000234693" "ENSG00000124171" "ENSG00000124243" "ENSG00000101126" [377] "ENSG00000259456" "ENSG00000000419" "ENSG00000124217" "ENSG00000232358" [381] "ENSG00000026559" $overGeneName [1] "FAM242B" "LINC01597" "AL121762.1" "AL121762.2" "FAM242A" [6] "DEFB115" "DEFB116" "DEFB118" "DEFB119" "DEFB121" [11] "DEFB123" "DEFB124" "REM1" "LINC00028" "HM13" [16] "AL110115.1" "MCTS2P" "HM13-IT1" "HM13-AS1" "AL110115.2" [21] "ID1" "COX4I2" "BCL2L1" "AL117381.1" "ABALON" [26] "TPX2" "MYLK2" "FOXS1" "DUSP15" "TTLL9" [31] "PDRG1" "XKR7" "AL031658.2" "AL031658.1" "CCM2L" [36] "HCK" "TM9SF4" "AL049539.1" "PLAGL2" "POFUT1" [41] "AL121897.1" "KIF3B" "AL121583.1" "ASXL1" "NOL4L" [46] "AL034550.1" "AL034550.3" "AL034550.2" "AL133343.2" "NOL4L-DT" [51] "AL133343.1" "C20orf203" "COMMD7" "DNMT3B" "MAPRE1" [56] "AL035071.2" "AL035071.1" "EFCAB8" "SUN5" "BPIFB2" [61] "BPIFB6" "BPIFB3" "BPIFB4" "BPIFA2" "AL121901.1" [66] "BPIFA3" "BPIFA1" "BPIFB1" "CDK5RAP1" "SNTA1" [71] "CBFA2T2" "AL121906.2" "NECAB3" "C20orf144" "ACTL10" [76] "AL121906.1" "E2F1" "PXMP4" "AL050349.1" "ZNF341" [81] "ZNF341-AS1" "CHMP4B" "RALY-AS1" "RALY" "AL031668.1" [86] "EIF2S2" "AL031668.2" "ASIP" "AL035458.2" "AHCY" [91] "AL356299.2" "ITCH" "ITCH-AS1" "ITCH-IT1" "AL109923.1" [96] "DYNLRB1" "MAP1LC3A" "PIGU" "NCOA6" "TP53INP2" [101] "AL109824.1" "GGT7" "ACSS2" "GSS" "MYH7B" [106] "TRPC4AP" "EDEM2" "PROCR" "AL356652.1" "MMP24OS" [111] "MMP24" "EIF6" "FAM83C-AS1" "FAM83C" "UQCC1" [116] "GDF5OS" "GDF5" "CEP250" "FO393401.1" "C20orf173" [121] "ERGIC3" "SPAG4" "CPNE1" "RBM12" "NFS1" [126] "ROMO1" "RBM39" "PHF20" "SCAND1" "CNBD2" [131] "NORAD" "AL035420.1" "AL035420.3" "AL035420.2" "EPB41L1" [136] "AL121895.1" "AL121895.2" "AAR2" "DLGAP4" "DLGAP4-AS1" [141] "MYL9" "TGIF2" "RAB5IF" "SLA2" "NDRG3" [146] "DSN1" "SOGA1" "TLDC2" "SAMHD1" "RBL1" [151] "AL136172.1" "MROH8" "RPN2" "GHRH" "MANBAL" [156] "AL034422.1" "SRC" "BLCAP" "NNAT" "AL109614.1" [161] "LINC01746" "LINC00489" "AL162293.1" "CTNNBL1" "VSTM2L" [166] "TTI1" "RPRD1B" "AL031651.1" "TGM2" "KIAA1755" [171] "AL031651.2" "AL359555.4" "AL359555.2" "AL359555.1" "BPI" [176] "LBP" "AL391095.2" "AL391095.1" "AL391095.3" "SNHG17" [181] "SNHG11" "RALGAPB" "ADIG" "ARHGAP40" "SLC32A1" [186] "ACTR5" "PPP1R16B" "FAM83D" "AL023803.2" "AL023803.1" [191] "DHX35" "AL023803.3" "LINC01734" "AL035251.1" "AL132981.1" [196] "AL118523.1" "LINC01370" "AL133419.1" "AL009050.1" "MAFB" [201] "AL035665.1" "AL035665.2" "TOP1" "PLCG1-AS1" "PLCG1" [206] "ZHX3" "LPIN3" "EMILIN3" "CHD6" "AL031667.3" [211] "AL049812.2" "AL049812.3" "PTPRT" "AL031656.1" "AL031676.1" [216] "AL021395.1" "SRSF6" "L3MBTL1" "Z98752.1" "SGK2" [221] "Z98752.4" "IFT52" "MYBL2" "GTSF1L" "LINC01728" [226] "TOX2" "JPH2" "AL035447.1" "OSER1" "OSER1-DT" [231] "GDAP1L1" "FITM2" "R3HDML" "AL117382.1" "HNF4A" [236] "HNF4A-AS1" "AL117382.2" "LINC01620" "TTPAL" "SERINC3" [241] "PKIG" "ADA" "LINC01260" "KCNK15-AS1" "CCN5" [246] "KCNK15" "AL118522.1" "RIMS4" "AL008725.1" "YWHAB" [251] "PABPC1L" "TOMM34" "STK4-AS1" "STK4" "KCNS1" [256] "WFDC5" "WFDC12" "PI3" "SEMG1" "SEMG2" [261] "SLPI" "MATN4" "RBPJL" "SDC4" "AL021578.1" [266] "SYS1" "TP53TG5" "DBNDD2" "PIGT" "AL031663.3" [271] "WFDC2" "AL031663.2" "SPINT3" "WFDC6" "EPPIN" [276] "WFDC8" "WFDC9" "WFDC10A" "WFDC11" "WFDC10B" [281] "WFDC13" "SPINT4" "WFDC3" "DNTTIP1" "UBE2C" [286] "TNNC2" "SNX21" "ACOT8" "ZSWIM3" "ZSWIM1" [291] "SPATA25" "NEURL2" "CTSA" "AL008726.1" "PLTP" [296] "AL162458.1" "PCIF1" "ZNF335" "MMP9" "SLC12A5-AS1" [301] "SLC12A5" "NCOA5" "CD40" "AL031687.1" "CDH22" [306] "SLC35C2" "AL133227.1" "ELMO2" "ZNF334" "OCSTAMP" [311] "SLC13A3" "AL133520.1" "TP53RK" "AL031055.1" "SLC2A10" [316] "EYA2" "AL354766.2" "ZMYND8" "AL031666.2" "AL031666.3" [321] "AL031666.1" "LINC01754" "NCOA3" "SULF2" "AL354813.1" [326] "AL357558.2" "AL357558.1" "AL357558.3" "LINC01522" "LINC01523" [331] "AL139351.2" "AL139351.3" "AL139351.1" "AL136102.1" "AL121888.2" [336] "AL121888.1" "LINC00494" "AL137078.1" "AL137078.2" "AL049541.1" [341] "AL049541.2" "PREX1" "AL035106.1" "AL133342.1" "ARFGEF2" [346] "CSE1L-AS1" "CSE1L" "STAU1" "DDX27" "ZNFX1" [351] "ZFAS1" "KCNB1" "PTGIS" "B4GALT5" "SLC9A8" [356] "SPATA2" "RNF114" "SNAI1" "TRERNA1" "UBE2V1" [361] "TMEM189" "LINC01275" "AL161937.1" "LINC01273" "CEBPB-AS1" [366] "CEBPB" "SMIM25" "LINC01270" "LINC01271" "PTPN1" [371] "AL133230.1" "RIPOR3" "AL353653.1" "PARD6B" "BCAS4" [376] "ADNP" "ADNP-AS1" "DPM1" "MOCS3" "AL050404.1" [381] "KCNG1" $Downstream_index [1] 1 > ### example 2 > GetCytoLocation(cyto_feature = "chr20") loading from cache Print out all cytogenetics features on chr20: c(20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 296, 297, 298, 299)c(1, 5100001, 9200001, 12000001, 17900001, 21300001, 22300001, 25700001, 28100001, 30400001, 33500001, 35800001, 39000001, 43100001, 43500001, 47800001, 51200001, 56400001, 57800001, 59700001, 1, 1, 1, 1)c(5100000, 9200000, 12000000, 17900000, 21300000, 22300000, 25700000, 28100000, 30400000, 33500000, 35800000, 39000000, 43100000, 43500000, 47800000, 51200000, 56400000, 57800000, 59700000, 64444167, 128386, 118774, 183433, 58661)c(21, 17, 16, 15, 9, 8, 7, 3, 100, 102, 103, 107, 108, 117, 118, 119, 120, 122, 123, 124, 1, 1, 1, 1)c(2, 6, 2, 6, 2, 4, 2, 1, 1, 2, 4, 2, 6, 2, 4, 2, 6, 2, 5, 2, 2, 2, 2, 2) $cytogeneticsInfo chr start end cytoband V5 1 chr20 1 5100000 p13 gneg 2 chr20 5100001 9200000 p12.3 gpos75 3 chr20 9200001 12000000 p12.2 gneg 4 chr20 12000001 17900000 p12.1 gpos75 5 chr20 17900001 21300000 p11.23 gneg 6 chr20 21300001 22300000 p11.22 gpos25 7 chr20 22300001 25700000 p11.21 gneg 8 chr20 25700001 28100000 p11.1 acen 9 chr20 28100001 30400000 q11.1 acen 10 chr20 30400001 33500000 q11.21 gneg 11 chr20 33500001 35800000 q11.22 gpos25 12 chr20 35800001 39000000 q11.23 gneg 13 chr20 39000001 43100000 q12 gpos75 14 chr20 43100001 43500000 q13.11 gneg 15 chr20 43500001 47800000 q13.12 gpos25 16 chr20 47800001 51200000 q13.13 gneg 17 chr20 51200001 56400000 q13.2 gpos75 18 chr20 56400001 57800000 q13.31 gneg 19 chr20 57800001 59700000 q13.32 gpos50 20 chr20 59700001 64444167 q13.33 gneg 21 chr20_GL383577v2_alt 1 128386 gneg 22 chr20_KI270869v1_alt 1 118774 gneg 23 chr20_KI270870v1_alt 1 183433 gneg 24 chr20_KI270871v1_alt 1 58661 gneg $Downstream_index [1] 0 > ### example 3 > GetCytoLocation(chr = "chr20", start = 25600000, end = 49800000) downloading 1 resources retrieving 1 resource loading from cache Error: failed to load resource name: AH53178 title: UCSC cytoBand track for hg38 reason: unknown input format Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ▆ 1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-partCNVH.R:3:3 2. ├─base::data.frame(AnnotationHub()[["AH53178"]]) 3. ├─AnnotationHub()[["AH53178"]] 4. └─AnnotationHub()[["AH53178"]] 5. └─AnnotationHub (local) .local(x, i, j = j, ...) 6. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 7. └─base::tryCatch(...) 8. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. └─value[[3L]](cond) [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted * 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: 2 ERRORs, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/partCNV.Rcheck/00check.log’ for details.