##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data KEGGREST
###
##############################################################################
##############################################################################


* checking for file ‘KEGGREST/DESCRIPTION’ ... OK
* preparing ‘KEGGREST’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘KEGGREST-vignette.Rmd’ using rmarkdown

Quitting from KEGGREST-vignette.Rmd:122-124 [keggGet]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (.self$lastField == "REFERENCE") ...`:
! missing value where TRUE/FALSE needed
---
Backtrace:
    ▆
 1. └─KEGGREST::keggGet(c("hsa:10458", "ece:Z5100"))
 2.   └─KEGGREST:::.getUrl(url, .flatFileParser)
 3.     ├─base::do.call(parser, list(content, ...))
 4.     └─KEGGREST (local) `<fn>`("ENTRY       10458             CDS       T01001\nSYMBOL      BAIAP2, BAP2, FLAF3, IRSP53, WAML\nNAME        (RefSeq) BAR/IMD domain containing adaptor protein 2\nORTHOLOGY   K05627  BAI1-associated protein 2\nORGANISM    hsa  Homo sapiens (human)\nPATHWAY     hsa04520  Adherens junction\n            hsa04810  Regulation of actin cytoskeleton\n            hsa05130  Pathogenic Escherichia coli infection\n            hsa05135  Yersinia infection\nNETWORK     nt06180  Pathogenic Escherichia coli\n  ELEMENT   N01094  Escherichia Eae/Tir/TccP to Actin signaling pathway\nBRITE       KEGG Orthology (KO) [BR:hsa00001]\n             09160 Human Diseases\n              09171 Infectious disease: bacterial\n               05130 Pathogenic Escherichia coli infection\n                10458 (BAIAP2)\n               05135 Yersinia infection\n                10458 (BAIAP2)\n             09180 Brite Hierarchies\n              09182 Protein families: genetic information processing\n               04131 Membrane trafficking [BR:hsa04131]\n                10458 (BAIAP2)\n            Membrane trafficking [BR:hsa04131]\n             Endocytosis\n              Bin/Amphiphysin/Rvs (BAR) family proteins\n               I-BAR proteins\n                10458 (BAIAP2)\nPOSITION    17:81035151..81117434\nMOTIF       Pfam: IMD SH3_2 SH3_9 SH3_1 BAR NDC80_loop Peptidase_Mx1 BAR_3\nDBLINKS     NCBI-GeneID: 10458\n            NCBI-ProteinID: NP_059345\n            OMIM: 605475\n            HGNC: 947\n            Ensembl: ENSG00000175866\n            UniProt: Q9UQB8\nSTRUCTURE   PDB\nAASEQ       552\n            MSLSRSEEMHRLTENVYKTIMEQFNPSLRNFIAMGKNYEKALAGVTYAAKGYFDALVKMG\n            ELASESQGSKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLSAAL\n            KKYQTEQRSKGDALDKCQAELKKLRKKSQGSKNPQKYSDKELQYIDAISNKQGELENYVS\n            DGYKTALTEERRRFCFLVEKQCAVAKNSAAYHSKGKELLAQKLPLWQQACADPSKIPERA\n            VQLMQQVASNGATLPSALSASKSNLVISDPIPGAKPLPVPPELAPFVGRMSAQESTPIMN\n            GVTGPDGEDYSPWADRKAAQPKSLSPPQSQSKLSDSYSNTLPVRKSVTPKNSYATTENKT\n            LPRSSSMAAGLERNGRMRVKAIFSHAAGDNSTLLSFKEGDLITLLVPEARDGWHYGESEK\n            TKMRGWFPFSYTRVLDSDGSDRLHMSLQQGKSSSTGNLLDKDDLAIPPPDYGAASRAFPA\n            QTASGFKQRPYSVAVPAFSQGLDDYGARSMSRNPFAHVQLKPTVTNDRCDLSAQGPEGRE\n            HGDGSARTLAGR\nNTSEQ       1659\n            atgtctctgtctcgctcagaggagatgcaccggctcacggaaaatgtctataagaccatc\n            atggagcagttcaaccctagcctccggaacttcatcgccatggggaagaattacgagaag\n            gcactggcaggtgtgacgtatgcagccaaaggctactttgacgccctggtgaagatgggg\n            gagctggccagcgagagccagggctccaaagaactcggagacgttctcttccagatggct\n            gaagtccacaggcagatccagaatcagctggaagaaatgctgaagtcttttcacaacgag\n            ctgcttacgcagctggagcagaaggtggagctggactccaggtatctgagtgctgcgctg\n            aagaaataccagactgagcaaaggagcaaaggcgacgccctggacaagtgtcaggctgag\n            ctgaagaagcttcggaagaagagccagggcagcaagaatcctcagaagtactcggacaag\n            gagctgcagtacatcgacgccatcagcaacaagcagggcgagctggagaattacgtgtcc\n            gacggctacaagaccgcactgacagaggagcgcaggcgcttctgcttcctggtggagaag\n            cagtgcgccgtggccaagaactccgcggcctaccactccaagggcaaggagctgctggcg\n            cagaagctgccgctgtggcaacaggcctgtgccgaccccagcaagatcccggagcgcgcg\n            gtgcagctcatgcagcaggtggccagcaacggcgccaccctccccagcgccctgtcggcc\n            tccaagtccaacctggtcatttccgaccccattccgggggccaagcccctgccggtgccc\n            cccgagctggcaccgttcgtggggcggatgtctgcccaggagagcacacccatcatgaac\n            ggcgtcacaggcccggatggcgaggactacagcccgtgggctgaccgcaaggctgcccag\n            cccaaatccctgtctcctccgcagtctcagagcaagctcagcgactcctactccaacaca\n            ctccccgtgcgcaagagcgtgaccccaaaaaacagctatgccaccaccgagaacaagact\n            ctgcctcgctcgagctccatggcagccggcctggagcgcaatggccgtatgcgggtgaag\n            gccatcttctcccacgctgctggggacaacagcaccctcctgagcttcaaggagggtgac\n            ctcattaccctgctggtgcctgaggcccgcgatggctggcactacggagagagtgagaag\n            accaagatgcggggctggtttcccttctcctacacccgggtcttggacagcgatggcagt\n            gacaggctgcacatgagcctgcagcaagggaagagcagcagcacgggcaacctcctggac\n            aaggacgacctggccatcccaccccccgattacggcgccgcctcccgggccttccccgcc\n            cagacggccagcggcttcaagcagaggccctacagtgtggccgtgcccgccttctcccag\n            ggcctggatgactatggagcgcggtccatgagcaggaatccctttgcccacgtccagctg\n            aagccgacagtgaccaacgacaggtgtgatctgtccgcccaagggccagaaggccgggag\n            cacggggatgggagcgcccgcaccctggctggaagatga\n///\n\nENTRY       Z5100             CDS       T00044\nSYMBOL      espF\nNAME        (GenBank) espF\nORTHOLOGY   K12786  LEE-encoded effector EspF\nORGANISM    ece  Escherichia coli O157:H7 EDL933 (EHEC)\nPATHWAY     ece05130  Pathogenic Escherichia coli infection\nMODULE      ece_M00542  EHEC/EPEC pathogenicity signature, T3SS and effectors\nBRITE       KEGG Orthology (KO) [BR:ece00001]\n             09160 Human Diseases\n              09171 Infectious disease: bacterial\n               05130 Pathogenic Escherichia coli infection\n                Z5100 (espF)\nPOSITION    complement(4658240..4658986)\nMOTIF       Pfam: EspF\nDBLINKS     NCBI-ProteinID: AAG58814\n            UniProt: A0A9Q7EE73\nAASEQ       248\n            MLNGISNAASTLGRQLVGIASRVSSAGGTGFSVAPQAVRLTPVKVHSPFSPGSSNVNART\n            IFNVSSQVTSFTPSRPAPPPPTSGQASGASRPLPPIAQALKEHLAAYEKSKGPEALGFKP\n            ARQAPPPPTSGQASGASRPLPPIAQALKEHLAAYEKSKGPEALGFKPARQAPPPPTSGQA\n            SGASRPLPPIAQALKEHLAAYEKSKGPEALGFKPARQAPPPPTGPSGLPPLAQALKDHLA\n            AYEQSKKG\nNTSEQ       747\n            atgcttaatggaattagtaacgctgcttctacactagggcggcagcttgtaggtatcgca\n            agtcgagtgagctctgcggggggaactggattttctgtagcccctcaggccgtgcgtctt\n            actccggtgaaagttcattcccctttttctccaggctcgtcgaatgttaatgcgagaacg\n            atttttaatgtgagcagccaggtgacttcatttactccctctcgtccggcaccgccgcca\n            ccgacaagtggacaggcatccggggcatcccgacctttaccgcccattgcacaggcatta\n            aaagagcacttggctgcctatgaaaaatcgaaaggtcctgaggctttaggttttaagccc\n            gcccgtcaggcaccgccgccaccgacaagtggacaggcatccggggcatcccgaccttta\n            ccgcccattgcacaggcattaaaagagcacttggctgcctatgaaaaatcgaaaggtcct\n            gaggctttaggttttaagcccgcccgtcaggcaccgccgccaccgacaagtggacaggca\n            tccggggcatcccgacctttaccgcccattgcacaggcattaaaagagcacttggctgcc\n            tatgaaaaatcgaaaggtcctgaggctttaggttttaagcccgcccgtcaggcaccaccg\n            ccaccgacagggcctagtggactaccgccccttgcacaggcattaaaagatcatttagct\n            gcctatgagcaatcgaagaaagggtaa\n///")
 5.       └─ffrec$setBody(value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'KEGGREST-vignette.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘KEGGREST-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘KEGGREST-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted